LMU BioDB 2013 - User contributions [en]

Kgosch Week 3

2013-09-19T19:29:48Z

Kgosch: added attempt at code for +1 sequence

cat sequence_file | ?????

'''Commands for Complement:'''

cat sequence_file | sed "y/atcg/tagc/"

'''Commands for Reading frames:(work in progress)'''

'''+1'''
cat sequence_file | sed "y/t/u/g" | sed "s/.../& /g" | sed -f ~dondi/xmlpipedb/data/genetic-code.sed

== Links ==
[[User:Kgosch|Kurt Gosch]]

[[Week 3|Assignment Page]]

[[Class Journal Week 3|Shared Journal]]

[[Category:Journal Entry]]

Kgosch Week 3

2013-09-19T04:02:31Z

Kgosch: re-added answer to first problem

cat sequence_file | ?????

'''Commands for Complement:'''

cat sequence_file | sed "y/atcg/tagc/"

'''Commands for Reading frames:'''

== Links ==
[[User:Kgosch|Kurt Gosch]]

[[Week 3|Assignment Page]]

[[Class Journal Week 3|Shared Journal]]

[[Category:Journal Entry]]

Kgosch Week 2

2013-09-19T00:22:16Z

Kgosch: added my week 2 corrections

'''Template:'''
5’-cgtatgctaataccatgttccgcgtataacccagccgccagttccgctggcggcatttta-3’
'''Complement:'''
3'-gcatacgattatggtacaaggcgcatattgggtcggcggtcaaggcgaccgccgtaaaat-5'

'''Reading Frames'''
:'''+1:''' N-Ter[ R(M)LIPCSAYNPAASSAGGIL ]C-Ter (Open Frame)
:'''+2:''' N-Ter[ VC(STOP)YHVPRITQPPVPLAAF ]C-Ter
:'''+3:''' N-Ter[ YANT(M)FRV(STOP)PSRQFRWRHF ]C-Ter
:'''-1:''' N-Ter[ N(STOP)PPRRSRRGLIRRTGYDYA ]C-Ter
:'''-2:''' N-Ter[ KVATAKVASGIHAKYWLRI ]C-Ter (Open Frame)
:'''-3:''' N-Ter[ KRRDGQGGVWYAGQV(M)ITH ]C-Ter (Open Frame)

'''Corrections'''

The 3' to 5' reading frames should appear as follows:
:'''-1:''' N-Ter[ (STOP)NAASGTGGWVIRGTWY(STOP)HT ]C-Ter
:'''-2:''' N-Ter[ K(M)PPAELAAGLYAEHGISI ]C-Ter (Open Frame)
:'''-3:''' N-Ter[ KCRQRNWRLGYTRN(M)VLAY ]C-Ter (Open Frame)

It turns out that I did correctly separate each group of three in the 3' to 5' direction, however my mistake was not reading the three letters within each group in that direction as well.

== Links ==
[[User:Kgosch|Kurt Gosch]]

[[Week 2|Assignment Page]]

[[Class Journal Week 2|Shared Journal]]

[[Category:Journal Entry]]

Kgosch Week 3

2013-09-16T06:23:36Z

Kgosch: created page and added links

== Links ==
[[User:Kgosch|Kurt Gosch]]

[[Week 3|Assignment Page]]

[[Class Journal Week 3|Shared Journal]]

[[Category:Journal Entry]]

Class Journal Week 3

2013-09-16T04:52:08Z

Kgosch: added my answers and entry (kgosch)

=='''[[user:kgosch|Kurt Gosch]]'''==
#I was able to successfully complete the ''Where's My Stuff?'' exercise. Everything behaved as I am used to in the past. However, I did find it interesting that while the file was still a '''.txt''' file, the TextEditor still read the html code and displayed the text as the code said to (with the bold, correct wordage, etc).
#Yes I connected to the Keck Lab successfully. However I had to change my password several times and have some assistance as the servers insisted my password was wrong (it wasn't).
#I believe I just simply need more practice and experience. Even though I know the basics of the command line and often use it for most of my classes, I hardly ever use it outside of school work.
[[User:Kgosch|Kgosch]] ([[User talk:Kgosch|talk]]) 21:52, 15 September 2013 (PDT)

=='''[[user:laurmagee|Lauren Magee]]'''==
# I was able to complete the "Where's Your Stuff?" exercise successfully. However, my TextEdit Program did not allow me to save my file with the extension .html. Instead, there was a drop down menu that allowed me to select the type of file I wanted to save my document as, and .html was included. Other than that, my computer was able to create the webpage as specified in the activity.
# I did succeed in connecting to the Keck lab. I found this task relatively easy compared to the other commands we use in different programs.
# I think my main problem with command lines, is that I can't remember the proper commands and what they produce. Using examples in class helps, because I am more likely to remember a code that I self typed and used to find an answer. Therefore, I think the most effective method in helping my retention of the information, would just be continue working through practice problems.
[[User:Laurmagee|Laurmagee]] ([[User talk:Laurmagee|talk]]) 12:43, 11 September 2013 (PDT)

=='''[[user:Kevinmcgee |Kevin McGee]]'''==
# I was able to complete "Where's Your Stuff?" fairly easily. I switched the file type from .txt to all files from a drop down menu and added the extension .html to the end of the title.
#I connected to the Keck Lab very easily.
#I feel that I just need more practice learning the command line. It is like another language, and takes time and practice to master.

[[Week 3]]

[[User:Kevinmcgee|Kevinmcgee]] ([[User talk:Kevinmcgee|talk]]) 15:03, 11 September 2013 (PDT)

=='''[[user:Ajvree|Alina Vreeland]]'''==
#I was able to complete the "where's your stuff?" exercise successfully. When I changed the extension to .html, the shortcut changed to a google chrome logo.
#I did have some trouble logging in to the Keck lab at first, but only because I forgot my username and password. After I figured out what that was, it was pretty simple.
#Practice is really all it takes. I think some sort of organized table or notes would help as a kind of reference guide until it becomes second nature using the different commands.

[[User:Ajvree|Ajvree]] ([[User talk:Ajvree|talk]]) 09:12, 12 September 2013 (PDT)<br>
[[Week 3]]

=='''[[user:Gleis|Gabriel Leis]]'''==
:#I completed the "Where's Your Stuff?" exercise unsuccessfully. In order to change the file to a .html file my computer insisted that I must first duplicate the document. After saving the file as .html the symbol next to the title did not change.
:#Success!!!!
:#I am still seeing blurred lines between the transition from a "normal" graphic file- i.e. word document- and a pure text file. Hopefully more practice with putty and terminal will define the lines.

[[User:Gleis|Gleis]] ([[User talk:Gleis|talk]]) 11:47, 12 September 2013 (PDT)

[[Category:Shared]]

[[Category:Journal Entry]]

==[[user:Taur.vil|Tauras]]==

#The computer did not act as expected for the "Where's Your Stuff?" exercise. I did it in Windows 8 which allows .s in file names without modifying the file type. As such, I was able to label the file .html but it remained a text file. However, I know what the expected outcome was and have found it does work that way changing photo file types (ex: jpeg to tiff) up until Vista.
#Yes, I was able to connect to the Keck lab.
#I need to just practice more and become familiar with the syntax. I would also like a large spreadsheet of common tasks as I feel frustrated at times with the piecemeal system. Even if only taught one technique at a time, it would be nice to have a reference that included many of them in an organized manner.

[[User:Taur.vil|Taur.vil]] ([[User talk:Taur.vil|talk]]) 21:25, 12 September 2013 (PDT)

=='''[[user:Lena|Lena Hunt]]'''==

1.) Did you complete the Where’s Your Stuff? exercise successfully (see below)? (by success, we mean that the computer behaved as described in that exercise) If things did not turn out as expected, what points do you think need further explaining or clarification?

Yes, I succeeded in completing the exercise. When I changed the document from a .txt file to an .html file, the icon changed on my screen. I have a mac, so it prominently displayed TXT or HTML on the icon, plus the icon looked like a miniature version of the document/webpage.

2.) Did you succeed in connecting to the Keck lab?

Yes, I did it the first week but forgot my password. Now I know how to make an account and reset the password, so I am all good.

3.) What do you think you need in order to grow more comfortable, confident, and effective with the command line and the practice tasks?
I think I just need practice. It is hard to remember all the commands and what each one does, but as long as I continue to use them and have a hardcopy showing me what they mean when I get stuck, I will muddle through.

:[[Lena Week 3]]

:17:59, 12 September 2013 (PDT)

=='''[[user:HDelgadi|Hilda Delgadillo]]'''==

*Did you complete the Where’s Your Stuff? exercise successfully? (by success, we mean that the computer behaved as described in that exercise) If things did not turn out as expected, what points do you think need further explaining or clarification?

I was able to complete the task; however I did run into some confusion since every time I saved the document with the .txt extension and then tried with the .html extension, the page would not open up as a web page. However, when I saved the file with a .html extension and did not save it with the .txt at all, I was able to see the results. I would say that the portion of saving the file with the different extensions needs more clarification to ultimately complete the task as stated in the directions.

*Did you succeed in connecting to the Keck lab?

I was indeed successful in connecting to the Keck lab.

*What do you think you need in order to grow more comfortable, confident, and effective with the command line and the practice tasks?

I think in order to feel more comfortable with the command line I need one on one orientation which means going to office hours, since I feel really unsure of how to become an effective learner. It is hard for me to follow along and also try to write notes as I try to catch up and make somewhat of a correlation to what I just learned, so that it can all make sense, all in a short amount of time. Office hours, here I come!

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 16:00, 12 September 2013 (PDT)

[[HDelgadi Week 3]]

=='''[[User:Ksherbina|Katrina Sherbina]]'''==

#I was successful in completing the "Where's ''Your'' Stuff exercise. When I opened the html version of the original text file, I saw two simple lines of text. The first stated "Hello File!" and the line directly beneath it stated "This is a text file that contains HTML".
#I was able to successfully connect to the Keck lab.
#While I did not feel too uncomfortable working with the command line this week, I think with some more practice using the different commands available, particularly through additional homework assignments, I will become quicker and more comfortable with using the command line.

[[User:Ksherbina|Ksherbina]] ([[User talk:Ksherbina|talk]]) 23:23, 12 September 2013 (PDT)

=='''[[User:Slouie|Stephen Louie]]'''==

#The computer responded successfully to the Where's ''Your'' Stuff exercise. When I changed the extension from .txt to .html, the notepad changed from a notepad to a web page.
#I successfully connected to Keck Lab.
#For something as complicated as this, plenty of repetition and experience with these tasks will help build confidence and knowledge. After a while, this proccess should become more fluid and less complicated.

[[User:Slouie|Slouie]] ([[User talk:Slouie|talk]]) 21:33, 12 September 2013 (PDT)

=='''[[User:Kmeilak|Kevin Meilak]]'''==

#I completed the Where’s Your Stuff exercise successfully, and the computer recognized the file as a website rather than a text file.
#I was able to successfully connect to the Keck lab.
#I need practice using all of the commands. Once I learn what each of them does well enough to not have to constantly look up their functions and effects, it will make me a much more effective user.

[[User:Kmeilak|Kmeilak]] ([[User talk:Kmeilak|talk]]) 19:52, 12 September 2013 (PDT)

==[[user: mpetredi | Mitchell Petredis]]==

#I was able to complete the Where’s Your Stuff? exercise successfully without any issues.
#I was able to connect to the Keck lab.
#I think I just need to get more familiar with the command codes in order to complete future assignments involving the command line much faster.

[[User:Mpetredi|Mpetredi]] ([[User talk:Mpetredi|talk]]) 22:06, 12 September 2013 (PDT)Mitchell Petredis

==[[User:dwilliams|Dillon Williams]]==

# I was able to complete the "Where's Your Stuff" exercise, however I initially had trouble with my computer allowing me to save the document as a .txt, and then I ran into trouble again when I tried to change it into a .html file because my computer did not want to allow me access to change the file.
# I was able to connect to the Keck Lab.
# I need to practice with command line more in order to be more comfortable with it.

-[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 22:28, 12 September 2013 (PDT)

[[Category: Shared Journal]]

== '''[[user: Vkuehn | Viktoria Kuehn]]''' ==
# I completed the Where's Your stuff" exercise without problems.
# I connected to the Keck lab easily, once I remembered my password.
# I think that I need to write down more direct steps, because I understand it in class but then I have some trouble repeating it on my own. I think just practicing is the best way to get more comfortable with using it.

[[Vkuehn Week 3]]
[[User:Vkuehn|Vkuehn]] ([[User talk:Vkuehn|talk]]) 07:14, 15 September 2013 (PDT)

User:Kgosch

2013-09-16T02:25:46Z

Kgosch: /* August 2011 - Present */ added degree date to current enrollment

:[https://www.facebook.com/kgosch www.facebook.com/kgosch]
:For the bio majors: [[Media:Intzillacopy.txt|My "scariest" java code]]

== Personal Info ==
[[Image: Kurtinplane.jpg|200px|thumb|right|What goes up...]]
Name:
Kurt Alan Gosch II

Email:
goschwork AT gmail DOT com

Address:
12963 Runway Rd. #410
Playa Vista, CA 90094

== Education ==

=== August 2004 - May 2009 ===

Loyola Marymount University

:*Graduated class of 2009
:*Bachelors degree in Film Production

=== August 2011 - Present ===

Loyola Marymount University

:*Currently enrolled
:*Bachelors degree in Computer Science
:*Degree to be finished in 2014

== Work Experience ==

=== Activision/Blizzard Inc ===

:'''Test Systems Engineer (Quality Assurance)'''
::*Functionality testing for game software and maintenance of found bugs database.
::*Assigned to high priority teams with strict deadlines and high work load.
::*Selected multiple times for new projects by request of project managers.

=== Paramount Studios ===

:'''Intern and personal assistant to Bobby Cohen'''
::*Worked in the post-production offices and alongside editors.
::*Experience both on and off the set for productions such as "Star Trek (2009)" and "Transformers:The Movie".

== Interests and Hobbies ==

:I can be summed up in the label of being a "gamer". I love to both play and work with games, both console/PC and physical boardgames. My hobbies include gaming, flying (I am currently earning my pilots license!), and nerding out with my friends over a wrestling match (WWE style, not the real stuff). I have a strong interest in the general field of science and love reading about new and exciting technologies and can't wait to see where the human race ends up in the future! 

== Assignments and Entries ==

[[Template:Kgosch]]

'''Assignment Pages'''
:[[Week 1 | Week 1]]
:[[Week 2 | Week 2]]
:[[Week 3 | Week 3]]
:[[Week 4 | Week 4]]
:[[Week 5 | Week 5]]
:[[Week 6 | Week 6]]
:[[Week 7 | Week 7]]
:[[Week 8 | Week 8]]
:[[Week 9 | Week 9]]
:[[Week 10 | Week 10]]
:[[Week 11 | Week 11]]
:[[Week 12 | Week 12]]
:[[Week 13 | Week 13]]
:[[Week 15 | Week 15]]

'''Shared Class Journal'''
:[[Class Journal Week 1 | Week 1]]
:[[Class Journal Week 2 | Week 2]]
:[[Class Journal Week 3 | Week 3]]
:[[Class Journal Week 4 | Week 4]]
:[[Class Journal Week 5 | Week 5]]
:[[Class Journal Week 6 | Week 6]]
:[[Class Journal Week 7 | Week 7]]
:[[Class Journal Week 8 | Week 8]]
:[[Class Journal Week 9 | Week 9]]

'''Personal Entries'''
:[[Kgosch Week 2 | Week 2]]
:[[Kgosch Week 3 | Week 3]]
:[[Kgosch Week 4 | Week 4]]
:[[Kgosch Week 5 | Week 5]]
:[[Kgosch Week 6 | Week 6]]
:[[Kgosch Week 7 | Week 7]]
:[[Kgosch Week 8 | Week 8]]
:[[Kgosch Week 9 | Week 9]]
:[[Kgosch Week 10 | Week 10]]
:[[Kgosch Week 11 | Week 11]]
:[[Kgosch Week 12 | Week 12]]
:[[Kgosch Week 13 | Week 13]]
:[[Kgosch Week 15 | Week 15]]

[[Category:User Page]]
[[Category:Awsome]]

User:Kgosch

2013-09-16T02:24:35Z

Kgosch: /* Interests and Hobbies */ removed line breaks

:[https://www.facebook.com/kgosch www.facebook.com/kgosch]
:For the bio majors: [[Media:Intzillacopy.txt|My "scariest" java code]]

== Personal Info ==
[[Image: Kurtinplane.jpg|200px|thumb|right|What goes up...]]
Name:
Kurt Alan Gosch II

Email:
goschwork AT gmail DOT com

Address:
12963 Runway Rd. #410
Playa Vista, CA 90094

== Education ==

=== August 2004 - May 2009 ===

Loyola Marymount University

:*Graduated class of 2009
:*Bachelors degree in Film Production

=== August 2011 - Present ===

Loyola Marymount University

:*Currently enrolled
:*Bachelors degree in Computer Science

== Work Experience ==

=== Activision/Blizzard Inc ===

:'''Test Systems Engineer (Quality Assurance)'''
::*Functionality testing for game software and maintenance of found bugs database.
::*Assigned to high priority teams with strict deadlines and high work load.
::*Selected multiple times for new projects by request of project managers.

=== Paramount Studios ===

:'''Intern and personal assistant to Bobby Cohen'''
::*Worked in the post-production offices and alongside editors.
::*Experience both on and off the set for productions such as "Star Trek (2009)" and "Transformers:The Movie".

== Interests and Hobbies ==

:I can be summed up in the label of being a "gamer". I love to both play and work with games, both console/PC and physical boardgames. My hobbies include gaming, flying (I am currently earning my pilots license!), and nerding out with my friends over a wrestling match (WWE style, not the real stuff). I have a strong interest in the general field of science and love reading about new and exciting technologies and can't wait to see where the human race ends up in the future! 

== Assignments and Entries ==

[[Template:Kgosch]]

'''Assignment Pages'''
:[[Week 1 | Week 1]]
:[[Week 2 | Week 2]]
:[[Week 3 | Week 3]]
:[[Week 4 | Week 4]]
:[[Week 5 | Week 5]]
:[[Week 6 | Week 6]]
:[[Week 7 | Week 7]]
:[[Week 8 | Week 8]]
:[[Week 9 | Week 9]]
:[[Week 10 | Week 10]]
:[[Week 11 | Week 11]]
:[[Week 12 | Week 12]]
:[[Week 13 | Week 13]]
:[[Week 15 | Week 15]]

'''Shared Class Journal'''
:[[Class Journal Week 1 | Week 1]]
:[[Class Journal Week 2 | Week 2]]
:[[Class Journal Week 3 | Week 3]]
:[[Class Journal Week 4 | Week 4]]
:[[Class Journal Week 5 | Week 5]]
:[[Class Journal Week 6 | Week 6]]
:[[Class Journal Week 7 | Week 7]]
:[[Class Journal Week 8 | Week 8]]
:[[Class Journal Week 9 | Week 9]]

'''Personal Entries'''
:[[Kgosch Week 2 | Week 2]]
:[[Kgosch Week 3 | Week 3]]
:[[Kgosch Week 4 | Week 4]]
:[[Kgosch Week 5 | Week 5]]
:[[Kgosch Week 6 | Week 6]]
:[[Kgosch Week 7 | Week 7]]
:[[Kgosch Week 8 | Week 8]]
:[[Kgosch Week 9 | Week 9]]
:[[Kgosch Week 10 | Week 10]]
:[[Kgosch Week 11 | Week 11]]
:[[Kgosch Week 12 | Week 12]]
:[[Kgosch Week 13 | Week 13]]
:[[Kgosch Week 15 | Week 15]]

[[Category:User Page]]
[[Category:Awsome]]

User:Kgosch

2013-09-16T02:22:30Z

Kgosch: /* Assignments and Entries */ added links to future assignment pages and submissions

:[https://www.facebook.com/kgosch www.facebook.com/kgosch]
:For the bio majors: [[Media:Intzillacopy.txt|My "scariest" java code]]

== Personal Info ==
[[Image: Kurtinplane.jpg|200px|thumb|right|What goes up...]]
Name:
Kurt Alan Gosch II

Email:
goschwork AT gmail DOT com

Address:
12963 Runway Rd. #410
Playa Vista, CA 90094

== Education ==

=== August 2004 - May 2009 ===

Loyola Marymount University

:*Graduated class of 2009
:*Bachelors degree in Film Production

=== August 2011 - Present ===

Loyola Marymount University

:*Currently enrolled
:*Bachelors degree in Computer Science

== Work Experience ==

=== Activision/Blizzard Inc ===

:'''Test Systems Engineer (Quality Assurance)'''
::*Functionality testing for game software and maintenance of found bugs database.
::*Assigned to high priority teams with strict deadlines and high work load.
::*Selected multiple times for new projects by request of project managers.

=== Paramount Studios ===

:'''Intern and personal assistant to Bobby Cohen'''
::*Worked in the post-production offices and alongside editors.
::*Experience both on and off the set for productions such as "Star Trek (2009)" and "Transformers:The Movie".

== Interests and Hobbies ==

:I can be summed up in the label of being a "gamer". I love to both play
:and work with games, both console/PC and physical boardgames. My hobbies
:include gaming, flying (I am currently earning my pilots license!), and
:nerding out with my friends over a wrestling match (WWE style, not the real stuff).
:I have a strong interest in the general field of science and love reading about
:new and exciting technologies and can't wait to see where the human race ends
:up in the future! 

== Assignments and Entries ==

[[Template:Kgosch]]

'''Assignment Pages'''
:[[Week 1 | Week 1]]
:[[Week 2 | Week 2]]
:[[Week 3 | Week 3]]
:[[Week 4 | Week 4]]
:[[Week 5 | Week 5]]
:[[Week 6 | Week 6]]
:[[Week 7 | Week 7]]
:[[Week 8 | Week 8]]
:[[Week 9 | Week 9]]
:[[Week 10 | Week 10]]
:[[Week 11 | Week 11]]
:[[Week 12 | Week 12]]
:[[Week 13 | Week 13]]
:[[Week 15 | Week 15]]

'''Shared Class Journal'''
:[[Class Journal Week 1 | Week 1]]
:[[Class Journal Week 2 | Week 2]]
:[[Class Journal Week 3 | Week 3]]
:[[Class Journal Week 4 | Week 4]]
:[[Class Journal Week 5 | Week 5]]
:[[Class Journal Week 6 | Week 6]]
:[[Class Journal Week 7 | Week 7]]
:[[Class Journal Week 8 | Week 8]]
:[[Class Journal Week 9 | Week 9]]

'''Personal Entries'''
:[[Kgosch Week 2 | Week 2]]
:[[Kgosch Week 3 | Week 3]]
:[[Kgosch Week 4 | Week 4]]
:[[Kgosch Week 5 | Week 5]]
:[[Kgosch Week 6 | Week 6]]
:[[Kgosch Week 7 | Week 7]]
:[[Kgosch Week 8 | Week 8]]
:[[Kgosch Week 9 | Week 9]]
:[[Kgosch Week 10 | Week 10]]
:[[Kgosch Week 11 | Week 11]]
:[[Kgosch Week 12 | Week 12]]
:[[Kgosch Week 13 | Week 13]]
:[[Kgosch Week 15 | Week 15]]

[[Category:User Page]]
[[Category:Awsome]]

Kgosch Week 2

2013-09-07T23:42:42Z

Kgosch: created page and added answers and links

Class Journal Week 2

2013-09-07T22:45:06Z

Kgosch: added my week 2 answers

=='''[[user:Kgosch|Kurt Gosch]]'''==
#The biggest discovery I made from these readings was definitely the extent to which bacteria was used to discover and understand the genetic code. It may be a little pretentious of me, but I had always thought as anything DNA related to have been found through studying humans alone. However, it obviously makes perfect sense to use bacteria as the source of study, since they are simpler, easy to reproduce, etc.
#Most of the Article ''Deciphering the Genetic Code'' was difficult for me to understand. There was a large volume of terms that I had no idea what they meant. Some I googled, some I just gave up on. The writing style in general was also not ideal, as the author tended to wander from topic to topic, the information within could have easily been conveyed in perhaps half as many words.
#From what I could understand, it seemed that it was discovered thought a long and painful process of trial and error. Various combinations of mRNA were mixed together and every time a successful bonding with amino acids took place it was recorded, until all 64 combinations had been found.
#The genetic code is basically the same as a computer code. The molecules are the 1's and 0's and the way that they combine together as DNA is the language (like Java, C++, or Ruby for a computer). Just like in a computer code, the smallest change in how the words(letters) are put together can have massive impact on what the code does. The best example from the readings is from the last article, when the author states that "errors can mean that embryos fail to develop at all - a fatal flaw in the operating system that causes the human system to crash as it boots up".

[[User:Kgosch|Kgosch]] ([[User talk:Kgosch|talk]]) 15:45, 7 September 2013 (PDT)

=='''[[user:Ajvree|Alina Vreeland]]'''==
*''What is the biggest discovery that I made from these readings?''
:Before reading the Nirenberg article, I had not been familiar with the idea of cell-free synthesis. Being able to create and manipulate proteins without an actual living cell is quite amazing, and I'm impressed by new technologies in the field that I am constantly learning about.
*''What part of the reading did I understand the least?''
:I didn't understand a lot of the processes described in the Nirenberg reading. I continually had to look up certain compounds or terminology that was used in order to get a feel for what was going on. While the process of discovering how the genetic code worked was interesting, the article itself was tedious to get through.
*''How was the genetic code solved experimentally?''
:First, polynucleotides were synthesized and put into a series of random orders and proportions. After all of them were synthesized, they tested how each would react to one out of twenty tRNA samples, and whether binding would occur. Then the start and stop codon were discovered, which gave way to being able to decipher the genetic code.
*''What is the relationship between the genetic code and a computer code?''
:Genetic code and computer code are very similar in nature. Each have a certain number of inputs that can be paired or strung together in order to achieve a certain output or task. The genetic code has nucleotides that form triplets to code for an end product of proteins, while computer code uses binary, etc, to run a program.
[[User:Ajvree|Ajvree]] ([[User talk:Ajvree|talk]]) 23:01, 5 September 2013 (PDT)
[[User:Ajvree|User Page]]

=='''[[user:mmalefyt|Miles Malefyt]]'''==
:*'''What is the biggest discovery that I made from these readings?'''
:The most interesting part of the readings came from the Hayes article where it was determined that only 114 out of a million codes were better than our genetic code already in place. This made me think that over the lifetime of genetic evolution, the code now used in our genes is
:*'''What part of the reading did I understand the least?'''
:The part that I understood the least came from the Moody paper where he compared the four different amino acids as essentially a binary code. I was under the impression that it was pretty important if a nucleotide was either an A or a G and that they couldn't be interchanged
:*'''How was the genetic code solved experimentally?'''
:A scientist named Nirenburg took all the mRNA and observed which amino acids they all translated into
:*'''What is the relationship between genetic code and computer code?'''
:The relationship between the genetic code and a computer code can be viewed as an input-output relationship. A certain code goes in and a specific result comes out. A single codon is like that of a line of code where individually it just makes an amino acid but together and in the right order they form a specific protein, or in coding, a program
=='''[[user:Lena|Lena Hunt]]'''==
:
:
:*'''What is the biggest discovery that I made from these readings?'''
:
:The biggest discovery I made from these readings came from the Hayes article. I thought that it would make sense that because DNA has to fit into the nucleus of a cell that it would have to be very information dense, but learning that DNA actually has extra nucleotides to buffer the effect of mutation and mistranslations was a revelation. I knew about introns and exons, but before now I didn't understand why introns existed.
:
:*'''What part of the readings did I understand the least?'''
:
:I didn't particularly understand the Nirenberg article. He referred to a lot of organic chemicals that I was unfamiliar with, and the pace of the writing left me glassy-eyed. I think that if I was more familiar with the types of tests he was performing that I would have been more engaged.
:
:*'''How was the genetic code solved experimentally?'''
:
:Nirenberg sythesized mRNA and observed which amino acids resulted from a given input.
:
*'''What is the relationship between the genetic code and a computer code?'''
:
:DNA encodes "lines of programming," a message composed of nucleotides that needs to be "run." A section of DNA in transcribed, just as computers transcribe sections of a program on a disk. In both computers and cells, the transcribed pieces are sent to different parts of the system. In cells, mRNA is translated into amino acids which become proteins, while in computers digital data is translated into analog output.
:
:[[User:Lena|Lena]] ([[User talk:Lena|talk]]) 23:00, 3 September 2013 (PDT)

=='''[[user:Kevinmcgee|Kevin McGee]]'''==

#What is the biggest discovery that I made from these readings?

:*I thought it was extremely interesting how Moody compared computer hackers to Nirenberg’s experiment. He would construct his own mRNA codons and watch what amino acids they would make as he imputed them. This is similar to computer hackers, who learn about knew computer systems by imputing information and watch what happens.

#What part of the readings did I understand the least?

:*I found the Nirenberg article to be very confusing. It was very heavy in its science and involved many procedures and language that I was unfamiliar with. I was able to grasp the big picture of the article, but I had trouble following the details

#How was the genetic code solved experimentally?

:*Nirenberg synthesized all 64 RNA codons, and looked at what amino acids were given from the codons.

#What is the relationship between the genetic code and a computer code?

:*The genetic code holds an extremely large amount of information and it is encoded through 4 nucleotides. A computer code tells a computer a large amount of information through the use of 2 numbers, 1’s and 0’s. The nucleotides tell the code for the cells, and the numbers tell the code for computer commands.

[[User:Kevinmcgee|Kevinmcgee]] ([[User talk:Kevinmcgee|talk]]) 19:38, 4 September 2013 (PDT)

[[Category:Shared]][[Category:Journal Entry]]

=='''[[user:laurmagee|Lauren Magee]]'''==
===Reading Reflection Questions===
# The biggest discovery that I made from these readings was how extensive the process was in initially solving of the genetic code. Now that the genetic code has been established, I think in modern day research of genetics, we take it for granted, because we are constantly moving on to the next discovery. As someone how has been involved in genetics research and plans on going into the field of genetics, I wasn't aware of who solved the genetic code and of all the work that lead to it.
# I've always had trouble understand the molecular processes of genetics. The central dogma is easy enough to understand, but beyond that is always difficult for me to picture. This includes identifying the important areas before the start codon or after the stop codon and determining which strand is the template. I think it'll just take some practice, because I find cell functions much harder to comprehend and retain compared to the other aspect of genetics.
# The genetic code was solved by Marshall Nirenberg as he translated the 64 possible messenger RNA codons (mRNA) into the appropriate amino acid they code for.
#The genetic code is similar to a computer code in that it is the informational ground work for a whole system. A computer code allows for the greater machine that is a computer to function in a proper and efficient manner, just as a genetic code allows for a cell to function in the same way for the greater machine that is our bodies.

===Genetic Code===
* 5'-CGTATGCTAATACCATGTTCCGCGTATAACCCAGCCGCCAGTTCCGCTGGCGGCATTTTA-3' -template strand
* 3'-GCATACGATTATGGTACAAGGCGCATATTGGGTCGGCGGTCAAGGCGACCGCCGTAAAAT-5' -complementary strand
*1st reading frame (+1): R-M (start)-L-I-P-C-S-Y-N-P-A-A-S-S-A-G-G-I-L: open reading frame (no stop codon included)
*2nd reading frame (+2): V-C-(stop)-Y-H-V-P-R-I-T-Q-P-P-V-P-L-A-A-F: stop codon included
*3rd reading frame (+3): Y-A-N-T-M (start)-F-R-V-(stop)-P-S-R-Q-F-R-W-P-H-F: stop codon included
*4th reading frame (-1): (stop)-N-A-A-S-G-T-G-G-W-V-I-R-G-T-W-Y-(stop)-H-T: stop codon included
*5th reading frame (-2): K-(start)-P-P-A-E-L-A-G-L-Y-A-E-H-G-I-S-I: open reading frame (no stop codon included)
*6th reading frame (-3): K-C-R-Q-R-N-W-L-G-Y-T-R-N-(start)-V-L-A-Y: open reading frame (no stop codon included)

[[User:Laurmagee|Laurmagee]] ([[User talk:Laurmagee|talk]]) 23:49, 5 September 2013 (PDT)

=='''[[User:Gleis|Gabriel Leis]]'''==

#The biggest discovery that I made from these readings was the concentration of protein in a cell as described by Brown in the NCBI article. As a biochemistry student I focus my attention on these molecules on the atomic level so often that I lose scope of the number of these molecules in organisms.
#I understood sections of the Nirenberg article the least. A lot of topic specific information was needed to fully understand the article.
#The Genetic Code was developed in two primary ways. The first was through analysis of the protein products derived from known sequences of artificial mRNA using cell free protein synthesizing systems. The second method involved the evaluation of a sensitive ribosome assay to see which amino acids associated with which RNA sequences.
#The genetic code is essentially is essentially the link between mRNA (program lines) and amino acids (the output). The ribosome acts like the CPU as machinery to translate the program lines into an output but the Genetic Code is what guides the translation machinery.

[[User:Gleis|Gleis]] ([[User talk:Gleis|talk]]) 21:33, 4 September 2013 (PDT)

==[[User:Taur.vil|Tauras]]==
#I was most interested in the comparison between DNA and computer code made in the Moody article and how the quaternary of the genetic code could be converted to two digit binary code. I've always heard DNA referred to as the genetic code, but had not thought before about the possibility of converting it into computer code.
#Like many of my classmates, I understood the Nirenburg article the least. He included a lot of technical language that did not make much sense to me, especially about his earlier research and the terms he used to describe his research.
#The genetic code was solved as Nirenburg (and Martin) synthesized trinucleotides and then determined what amino acid each trinucleotide added to a protein chain.
#The genetic code can be translated into computer code by using a di-digit binary system to represent the four amino acids. Like computer code, genetic code gives the instructions for specialized program output which is translated by different cells (computer equivalents) to produce proteins and working machinery.

-[[User:Taur.vil|Taur.vil]] ([[User talk:Taur.vil|talk]]) 23:16, 4 September 2013 (PDT)

==[[User:Slouie|Stephen Louie]]==
#I was intrigued at the relationship shared between computer code and DNA. For the most part, I was relatively familiar with the biological aspect of DNA. However, I never considered the possibility of DNA being translated into something that can be input as a program. I am sincerely intrigued at the aspect of using digital technology to research and modify the human genome in the form of a code.
#The historical review article was slightly confusing to me. From prior knowledge, I had a good idea at the type of work the author was performing. However, I was unfamiliar with several parts of the article when he went into greater detail. I feel that I would have a better understanding of this article, if I had taken more upper division biology courses.
#The 64 trinucleotides of known sequences were used to determine what nucleotide input created what amino acid.
#Genetic code is similar to computer code in that they are both command instructions that determine the actions of a machine, whether it is a organism or a computer program. Genetic code can also be translated into a binary sequence with A being 00, C being 01, G being 10, and T being 11.
[[User:Slouie|Slouie]] ([[User talk:Slouie|talk]]) 05:46, 5 September 2013 (PDT)

{{mpetredi Week 2 Journal Entry}}

==[[User:Kmeilak|Kevin Meilak]]==

#The biggest discovery I made from these readings was how the genetic code was cracked experimentally. I had previously learned about how it was thought at the time that protein was the genetic material, not DNA, but never imagined how long the experiments took or how difficult it was to demonstrate that mRNA caused the incorporation of amino acids into protein.
#The most difficult part of the readings was some of the experimental procedures in the Nirenberg reading. Despite a background in biology, experimental procedure from a biochemistry perspective was discussed little, even for processes as significant in biology as replication, transcription, and translation.
#The genetic code was cracked in several steps. After it was discovered that DNA, not protein, was the genetic material, the next logical step was to discover how it translated itself into protein and RNA. First, it was discovered that mRNA was the molecule that served as an intermediate between DNA and protein. The existence of this intermediate demonstrated that DNA did not, or could not, directly translate itself into protein. Then it was discovered that the code was read in triplets “by the amounts of radioactive histidine, threonine, asparagine, glutamine, lysine and proline that were incorporated into protein by ﬁve poly(A-C) preparations that contained different ratios of A and C” (Nirenberg, 50). Then, each possible trinucleotide combination was mixed with the 20 different tRNAs to determine which amino acid was coded for by each trinucleotide.
#The genetic code is like a computer code in that both at digital; the base pairs adenine, guanine, thymine, and cytosine do not code for protein because of inherent chemical properties but rather in how they relate to each other. The Moody reading demonstrated that substituting 00, 01, 10, and 11 for each nucleotide produced the same effect as A, T, C, G. The importance is how they are read, not what they are.

[[User:Kmeilak|Kmeilak]] ([[User talk:Kmeilak|talk]]) 17:22, 5 September 2013 (PDT)

==[[User:dwilliams|Dillon Williams]]==

#The biggest discovery that I made from these readings was the particular process in which the genetic code was solved. I had never actually read the process of how the code was cracked before this article.
# I found the Nirenburg article to be very confusing based on the language that he was using as well as the multiple references to things that I didn't have any previous knowledge of, as a result it was fairly difficult to follow.
#The genetic code was solved by Nirenburg, who synthesized trinucleotides and then determined which amino acid each trinucleotide added to a given protein chain.
#Much like computer code, genetic code can be translated into a formulaic system using binary. This code is then read based on how the nucleotide sequences are read, allowing the body to respond to the function in the code.

-[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 20:05, 5 September 2013 (PDT)

=='''[[User:Ksherbina|Katrina Sherbina]]'''==

#In going through the assigned readings, I was most intrigued by Hayes's discussion at the end of his paper about the different conjectures that scientists have as to why 64 codons evolved to code for 20 amino acids. As the hypothesis diverges significantly from what I have been taught, I was struck by the idea that this may be a result of an ancient mechanism of translation by which both strands of DNA were read simultaneously.
#I had some difficulty reading through the paper by Nirenberg. I found myself pausing several times to look up unfamiliar terms and reread sections in order to understand the different types of experiments that Nirenberg discussed in the paper. In contrast, the other readings were less technical and, thus, easier to read.
#By performing cell-free protein synthesis using randomly ordered polynucleotides composed of different ratios of nucleotides, Nirenberg, with the help of other scientists, deduced that the genetic code consists of codons composed of three nucleotides. This led to the idea that there are 64 possible codons. The sequence of each of the possible codons was matched to an amino acid by synthesizing each of the 64 codons and testing each one against 20 different radioactive amino-acyl tRNAs.
#The genetic code, like computer code, is essentially a set of instructions that is processed to produce a specific output. As mentioned in the paper by Moody, both codes consist of discrete signals: the four nucleotides make up the genetic code and sequences of 1's and 0's form computer code. The genetic code can be written in binary by assigning one of the four binary digits 00, 01, 10, or 11 to each one of the nucleotides.

[[User:Ksherbina|Ksherbina]] ([[User talk:Ksherbina|talk]]) 22:18, 5 September 2013 (PDT)

=='''[[User:HDelgadi|Hilda Delgadillo]]'''==

'''''What is the biggest discovery that I made from these readings?'''''

*The biggest discovery I made from these readings was the fact that tRNA was discovered before mRNA as read in Nirenberg’s personal account, so in a way we approached the synthesis of proteins in reverse, from translation to transcription.

'''''What part of the readings did I understand the least?'''''

*I couldn't really understand why there was so much importance to the almost insoluble polyphenylalanine which as Nirenberg mentions, is soluble in 15% hydrobromic acid dissolved in concentrated acetic acid, and why was it necessary (Nirenberg, 49)?

'''''How was the genetic code solved experimentally?'''''

*Nirenberg and his colleagues were able to make different combinations of polynucleotides and were able to see the results of their matches with what the polynucleotides yielded in terms of amino acids.

'''''What is the relationship between the genetic code and a computer code?'''''

*The genetic code is like a computer code due to its ability of handling all types of “programs” within the body. The genetic code is crucial for the function of the human being, so it is the software of the body as computers are in need of operating system software to continue their function.

[[User: HDelgadi| Hilda Delgadillo]]

[[Template: HDelgadi]]

==[[User:Vkuehn|Viktoria Kuehn]]==

*What is the biggest discovery that I made from these readings?
The thing that I found surprising about the readings is the way Mendel's work was so under appreciated and ignored when they were in search of answers to genetic and hereditary questions. His work is taught to everyone studying biology today and was so methodical and accurate that it is surprising that people did not pay more attention to it when it was published.
*What part of the readings did I understand the least?
I had the most trouble understanding the details in the Nirenberg reading. It was very dense with biochemical details of the experiment and this made it hard to follow, there were a lot of specifics that it referenced about the processes that made it difficult. It was interesting to read about an on hand account of what happened though, even if I did not understand all the details fully.
*How was the genetic code solved experimentally?
After deciding that DNA was responsible for the genetic code, not proteins, Nirenberg used a way of trial and error by experimenting with the base compostions of RNA codons by combining different polynucleotides with different proportions of nucleotides to see what amino acids resulted.
*What is the relationship between the genetic code and a computer code?
I think that the most fundamental like between the genetic code and a computer code is the way that they transmit information. So many proccesses in the body are driven by biological factors through physical or chemical signals, but genes are encoded in a very unique way. They are in the form of a code that other parts of the cell can regognize and respond to in a specific way. This is also the case for computer code; there is a set of guidelines that the computer always carries out when presented with a code that it recognizes.

[[User:Vkuehn|Vkuehn]] ([[User talk:Vkuehn|talk]]) 23:43, 5 September 2013 (PDT)

User:Kgosch

2013-09-06T06:34:11Z

Kgosch: /* Assignments and Entries */ added week 2 and personal section

Template:Kgosch

2013-09-06T06:30:31Z

Kgosch: /* Links */

== Links ==
[[User:Kgosch|Kurt Gosch]]

[[Week 1|Assignment Page]]

[[Class Journal Week 1|Shared Journal]]

[[Category:Journal Entry]]

Template:Kgosch

2013-09-06T06:20:06Z

Kgosch: created the template for hw and links

== Links ==
[[User:Kgosch|Kurt Gosch]]

[[Week 1|Assignment Page]]

[[Personal Journal Week 1|Personal Journal]]

[[Class Journal Week 1|Shared Journal]]

[[Category:Journal Entry]]

User:Kgosch

2013-09-06T06:11:19Z

Kgosch: /* Assignments and Entries */ added template link

User:Kgosch

2013-09-06T06:04:22Z

Kgosch: added catagories to the bottom of the page (stole "user page" idea from Dondi's)

User:Kgosch

2013-09-06T06:00:17Z

Kgosch: uploaded txt file with "scary" java code

File:Intzillacopy.txt

2013-09-06T05:56:52Z

Kgosch: For the bio-majors, my "scariest looking" java code

For the bio-majors, my "scariest looking" java code

User:Kgosch

2013-09-06T05:49:19Z

Kgosch: added a photo of myself

:[https://www.facebook.com/kgosch www.facebook.com/kgosch]

== Personal Info ==
[[Image: Kurtinplane.jpg|200px|thumb|right|What goes up...]]
Name:
Kurt Alan Gosch II

Email:
goschwork AT gmail DOT com

Address:
12963 Runway Rd. #410
Playa Vista, CA 90094

== Education ==

=== August 2004 - May 2009 ===

Loyola Marymount University

:*Graduated class of 2009
:*Bachelors degree in Film Production

=== August 2011 - Present ===

Loyola Marymount University

:*Currently enrolled
:*Bachelors degree in Computer Science

== Work Experience ==

=== Activision/Blizzard Inc ===

:'''Test Systems Engineer (Quality Assurance)'''
::*Functionality testing for game software and maintenance of found bugs database.
::*Assigned to high priority teams with strict deadlines and high work load.
::*Selected multiple times for new projects by request of project managers.

=== Paramount Studios ===

:'''Intern and personal assistant to Bobby Cohen'''
::*Worked in the post-production offices and alongside editors.
::*Experience both on and off the set for productions such as "Star Trek (2009)" and "Transformers:The Movie".

== Interests and Hobbies ==

:I can be summed up in the label of being a "gamer". I love to both play
:and work with games, both console/PC and physical boardgames. My hobbies
:include gaming, flying (I am currently earning my pilots license!), and
:nerding out with my friends over a wrestling match (WWE style, not the real stuff).
:I have a strong interest in the general field of science and love reading about
:new and exciting technologies and can't wait to see where the human race ends
:up in the future! 

== Assignments and Entries ==

'''Shared Class Journal'''
:[[Class Journal Week 1 | Week 1]]

File:Kurtinplane.jpg

2013-09-06T05:41:35Z

Kgosch: Picture of Kurt Gosch learning how to fly a plane!

Picture of Kurt Gosch learning how to fly a plane!

User:Kgosch

2013-09-06T05:37:55Z

Kgosch: added easter egg for GoT fans

:[https://www.facebook.com/kgosch www.facebook.com/kgosch]

== Personal Info ==

Name:
Kurt Alan Gosch II

Email:
goschwork AT gmail DOT com

Address:
12963 Runway Rd. #410
Playa Vista, CA 90094

== Education ==

=== August 2004 - May 2009 ===

Loyola Marymount University

:*Graduated class of 2009
:*Bachelors degree in Film Production

=== August 2011 - Present ===

Loyola Marymount University

:*Currently enrolled
:*Bachelors degree in Computer Science

== Work Experience ==

=== Activision/Blizzard Inc ===

:'''Test Systems Engineer (Quality Assurance)'''
::*Functionality testing for game software and maintenance of found bugs database.
::*Assigned to high priority teams with strict deadlines and high work load.
::*Selected multiple times for new projects by request of project managers.

=== Paramount Studios ===

:'''Intern and personal assistant to Bobby Cohen'''
::*Worked in the post-production offices and alongside editors.
::*Experience both on and off the set for productions such as "Star Trek (2009)" and "Transformers:The Movie".

== Interests and Hobbies ==

:I can be summed up in the label of being a "gamer". I love to both play
:and work with games, both console/PC and physical boardgames. My hobbies
:include gaming, flying (I am currently earning my pilots license!), and
:nerding out with my friends over a wrestling match (WWE style, not the real stuff).
:I have a strong interest in the general field of science and love reading about
:new and exciting technologies and can't wait to see where the human race ends
:up in the future! 

== Assignments and Entries ==

'''Shared Class Journal'''
:[[Class Journal Week 1 | Week 1]]

User:Kgosch

2013-09-06T05:36:01Z

Kgosch: changed a few sections to include bullet lists

:[https://www.facebook.com/kgosch www.facebook.com/kgosch]

== Personal Info ==

Name:
Kurt Alan Gosch II

Email:
goschwork AT gmail DOT com

Address:
12963 Runway Rd. #410
Playa Vista, CA 90094

== Education ==

=== August 2004 - May 2009 ===

Loyola Marymount University

:*Graduated class of 2009
:*Bachelors degree in Film Production

=== August 2011 - Present ===

Loyola Marymount University

:*Currently enrolled
:*Bachelors degree in Computer Science

== Work Experience ==

=== Activision/Blizzard Inc ===

:'''Test Systems Engineer (Quality Assurance)'''
::*Functionality testing for game software and maintenance of found bugs database.
::*Assigned to high priority teams with strict deadlines and high work load.
::*Selected multiple times for new projects by request of project managers.

=== Paramount Studios ===

:'''Intern and personal assistant to Bobby Cohen'''
::*Worked in the post-production offices and alongside editors.
::*Experience both on and off the set for productions such as "Star Trek (2009)" and "Transformers:The Movie".

== Interests and Hobbies ==

:I can be summed up in the label of being a "gamer". I love to both play
:and work with games, both console/PC and physical boardgames. My hobbies
:include gaming, flying (I am currently earning my pilots license!), and
:nerding out with my friends over a wrestling match (WWE style, not the real stuff).
:I have a strong interest in the general field of science and love reading about
:new and exciting technologies and can't wait to see where the human race ends
:up in the future!

== Assignments and Entries ==

'''Shared Class Journal'''
:[[Class Journal Week 1 | Week 1]]

User:Kgosch

2013-09-06T05:25:43Z

Kgosch: added external link to my FB page

:[https://www.facebook.com/kgosch www.facebook.com/kgosch]

== Personal Info ==

Name:
Kurt Alan Gosch II

Email:
goschwork AT gmail DOT com

Address:
12963 Runway Rd. #410
Playa Vista, CA 90094

== Education ==

=== August 2004 - May 2009 ===

Loyola Marymount University

:Graduated class of 2009
:Bachelors degree in Film Production

=== August 2011 - Present ===

Loyola Marymount University

:Currently enrolled
:Bachelors degree in Computer Science

== Work Experience ==

=== Activision/Blizzard Inc ===

:'''Test Systems Engineer (Quality Assurance)'''
::Functionality testing for game software and maintenance of
::found bugs database. Also assigned to high priority teams with
::strict deadlines and high work load. Selected multiple times
::for new projects by request of project managers.

=== Paramount Studios ===

:'''Intern and personal assistant to Bobby Cohen'''
::Worked in the post-production offices and alongside
::editors. Experience both on and off the set for productions
::such as "Star Trek (2009)" and "Transformers:The Movie".

== Interests and Hobbies ==

:I can be summed up in the label of being a "gamer". I love to both play
:and work with games, both console/PC and physical boardgames. My hobbies
:include gaming, flying (I am currently earning my pilots license!), and
:nerding out with my friends over a wrestling match (WWE style, not the real stuff).
:I have a strong interest in the general field of science and love reading about
:new and exciting technologies and can't wait to see where the human race ends
:up in the future!

== Assignments and Entries ==

'''Shared Class Journal'''
:[[Class Journal Week 1 | Week 1]]

User:Kgosch

2013-09-06T05:20:34Z

Kgosch: /* Assignments and Entries */

== Personal Info ==

Name:
Kurt Alan Gosch II

Email:
goschwork AT gmail DOT com

Address:
12963 Runway Rd. #410
Playa Vista, CA 90094

== Education ==

=== August 2004 - May 2009 ===

Loyola Marymount University

:Graduated class of 2009
:Bachelors degree in Film Production

=== August 2011 - Present ===

Loyola Marymount University

:Currently enrolled
:Bachelors degree in Computer Science

== Work Experience ==

=== Activision/Blizzard Inc ===

:'''Test Systems Engineer (Quality Assurance)'''
::Functionality testing for game software and maintenance of
::found bugs database. Also assigned to high priority teams with
::strict deadlines and high work load. Selected multiple times
::for new projects by request of project managers.

=== Paramount Studios ===

:'''Intern and personal assistant to Bobby Cohen'''
::Worked in the post-production offices and alongside
::editors. Experience both on and off the set for productions
::such as "Star Trek (2009)" and "Transformers:The Movie".

== Interests and Hobbies ==

:I can be summed up in the label of being a "gamer". I love to both play
:and work with games, both console/PC and physical boardgames. My hobbies
:include gaming, flying (I am currently earning my pilots license!), and
:nerding out with my friends over a wrestling match (WWE style, not the real stuff).
:I have a strong interest in the general field of science and love reading about
:new and exciting technologies and can't wait to see where the human race ends
:up in the future!

== Assignments and Entries ==

'''Shared Class Journal'''
:[[Class Journal Week 1 | Week 1]]

Main Page

2013-09-06T05:16:39Z

Kgosch: /* Students */ added link to Kurt Gosch personal page

__NOTOC__
<div style="text-align: center; font-size: 175%; margin-bottom: 0.85em">Loyola Marymount University</div>
<div style="text-align: center; font-size: 250%; line-height: 1.25em; margin-bottom: 1em">'''BIOL/CMSI 367-01/HNRS 398-01: Biological Databases'''</div>

<div class="toc-container">__TOC__</div>

== Announcements ==

=== Seminars and Events ===

* '''Bioethics Institute Annual Lecture:''' Tuesday, September 24, 7:00-8:30 PM, UH1000, Dr. Roberto Dell’Oro, Director of the LMU Bioethics Instiute, ''The Ethos of American Bioethics: Between Individual Liberalism and Social Solidarity''


=== Class Locations ===

* September 10: ''lab''
* September 12: ''lab''

=== Course Assessment ===

We ask that students in this class participate in the [http://www.grinnell.edu/academic/psychology/faculty/dl/risc/ Research on the Integrated Science Curriculum (RISC) Survey] which will allow the instructors to evaluate the effectiveness of this course. Please complete the [https://survey.grinnell.edu/se.ashx?s=2511374543A7A49D student pre-course survey], using "Dahlquist" as the instructor last name.

== Instructors ==
* [[User:Kdahlquist|Kam D. Dahlquist]]
* [[User:Dondi|John David N. Dionisio]]

== Students ==

{| style="width: 50%"
| [[User:HDelgadi| Hilda Delgadillo]]
| [[User:Gleis| Gabriel Leis]]
| [[User:kevinmcgee | Kevin McGee]]
| [[User:Taur.vil|Tauras Vilgalys]]
|-
| [[User:Kgosch | Kurt Gosch]]
| [[User:Slouie | Stephen Louie]]
| [[User:Kmeilak|Kevin Meilak]]
| [[User:Ajvree|Alina Vreeland]]
|-
| [[User:Lena | Lena Hunt]]
| [[User:laurmagee|Lauren Magee]]
| [[User:mpetredi|Mitchell Petredis]]
| [[User:Dwilliams|Dillon Williams]]
|-
| [[User:vkuehn|Viktoria Kuehn]]
| [[User:Mmalefyt|Miles Malefyt]]
| [[User:Ksherbina|Katrina Sherbina]]
|
|}

== Course Schedule ==

The current course schedule is shown below. In addition to the listed in-class agendas, the following guidelines are also notable:

* Unless otherwise stated on the schedule, your weekly journals/assignments are due on Fridays at midnight (Thursday night/Friday morning). In cases where subsequent revisions or corrections will be accepted, the instructors will provide feedback and submission deadlines on a per-assignment basis.
* Reading assignments should be completed ''before'' coming to class.
* Dr. Dionisio’s Tuesday and Thursday morning office hours can be viewed as unofficial lab sessions: use them for IT help or desktop support

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 1em; background: #ddd" | #
! style="width: 2em; background: #ddd" | Date
! style="width: 5em; background: #ddd" | Reading
! style="background: #ddd" | Agenda
! style="background: #ddd" | Journal
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right" | Tuesday<br/>8/27/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Syllabus walkthrough
* ''my.cs.lmu.edu'' account: Visit https://secure.cs.lmu.edu to get a computer science account if you don’t already have one
* Class wiki account: Set up a username and password for this wiki site

Pairwise interviews (report back after each bullet)
* Basic acquaintance information
* Like a cell/not like a cell; like a computer/not like a computer

| style="vertical-align: top; text-align: center" | [[Week 1]]

(due at midnight 8/30)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right; background: #eee" | Thursday<br/>8/29/2013
| style="vertical-align: top; background: #eee" |
[http://dl.acm.org/ft_gateway.cfm?id=1378711 ''Voices of Computing''] and [http://dl.acm.org/ft_gateway.cfm?id=1272529 ''Computing is a Natural Science''] by Peter Denning (these links should be accessed from within LMU to get the full article)

[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on MyLMUConnect)
| style="vertical-align: top; background: #eee" | Discuss the [[Week 1]] assignment (accounts should be ready to wiki at this point)
* Quick wiki overview
* User wiki page setup
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right" | Tuesday<br/>9/3/2013
| style="vertical-align: top" | [http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1.1 ''Genomes 2'']

[http://www.nature.com/nature/dna50/watsoncrick.pdf Watson & Crick (1953)]

[http://www.nature.com/nature/dna50/franklingosling.pdf Franklin & Gosling (1953)]

| style="vertical-align: top" | DNA
* DNA structure and Genetic Code
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class on MyLMU Connect]

| style="vertical-align: top; text-align: center" | [[Week 2]]

(due at midnight 9/6)

[[Class Journal Week 2]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right; background: #eee" | Thursday<br/>9/5/2013
| style="vertical-align: top; background: #eee" | On [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect]:

Nirenberg (2004) ''Deciphering the Genetic Code''

Moody (2004) ''Digital Code of Life'', Ch. 1

Hayes (2004) ''Ode to the Code''

[http://www.ncbi.nlm.nih.gov/books/NBK21121/ Ch. 3 ''Genomes 2''], Chapters 8-12, as needed for the final project
| style="vertical-align: top; background: #eee" | Central dogma

* [http://www.youtube.com/watch?v=u9dhO0iCLww Berkeley translation video]
* This [http://www.dnai.org/a/index.html web site] has links to animations of the replication, transcription, and translation processes.

* [[Media:20100914_CentralDogma.pdf | Slides shown in class]]
* [[Central Dogma Pencil Exercise]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right" | Tuesday<br/>9/10/2013
| style="vertical-align: top" | [http://myweb.lmu.edu/dondi/share/intro/wheres-my-stuff.pdf Where's my Stuff?]

[[Introduction to the Command Line]]
| style="vertical-align: top" | An overview of computers, networks, files, and databases
* Manipulating DNA sequences on the command line
* [[Using the XMLPipeDB Match Utility]] 
| style="vertical-align: top; text-align: center" | [[Week 3]]

(due at midnight 9/13)

[[Class Journal Week 3]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right; background: #eee" | Thursday<br/>9/12/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Command line lab session
* Hands-on practice
* Discuss [[Week 3]] assignment tasks
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right" | Tuesday<br/>9/17/2013
| style="vertical-align: top" | [[More Text Processing Features]]

[[How to Read XML Files]]

[[Media:Moody_DigitalCodeofLife_Ch6_04.pdf | Showing the Data]]

[http://www.nature.com/news/2010/100623/pdf/4651000a.pdf Science After the Sequence]

[http://www.nature.com/news/2010/100623/full/4651000a.html Nature Special: Human Genome at 10]
| style="vertical-align: top" | Command line lab session
* Review assignment issues
* Discuss [[Week 4]] computer portion

| style="vertical-align: top; text-align: center" | [[Week 4]]

(due at midnight 9/20)

[[Class Journal Week 4]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right; background: #eee" | Thursday<br/>9/19/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |Genome sequencing and annotation
* [[Media:20100921_HGP.pdf | Slides shown in class]]

| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right" | Tuesday<br/>9/24/2013
| style="vertical-align: top" |
[http://nar.oxfordjournals.org/content/41/D1/D1.full Introduction to ''NAR'' Database Issue]
| style="vertical-align: top" | [[Media:20100928_BiologicalDatabases.pdf | Introduction to biological databases]]
| style="vertical-align: top; text-align: center" | [[Week 5]]

(due at midnight 9/27)

[[Class Journal Week 5]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right; background: #eee" | Thursday<br/>9/26/2013
| style="vertical-align: top; background: #eee" |
[http://myweb.lmu.edu/dondi/share/db/relational1.pdf The Relational Data Model: Structure]

[http://myweb.lmu.edu/dondi/share/db/sql.pdf An Overview of SQL]

[http://myweb.lmu.edu/dondi/share/db/pgsql-quickstart.pdf PostgreSQL Quick Start]

[[PostgreSQL Tutorial]]
| style="vertical-align: top; background: #eee" | Introduction to relational databases
* [[PostgreSQL Tutorial]]
* Relating XML structure to relational structure
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right" | Tuesday<br/>10/1/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Database presentations
* [[Some Topics to Consider When Critiquing Talks]]
| style="vertical-align: top; text-align: center" | [[Week 6]]

(due at midnight 10/4)

[[Class Journal Week 6]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right; background: #eee" | Thursday<br/>10/3/2013
| style="vertical-align: top; background: #eee" | Additional background and details can be found in Chapters 1, 2, and 6 of ''A First Course in Database Systems'' (on reserve at the library).
| style="vertical-align: top; background: #eee" | SQL and working with relational databases continued
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right" | Tuesday<br/>10/8/2013
| style="vertical-align: top" | [[Media:Brown_NatGenet_99_microarrays.pdf | Brown_NatGenet_99_microarrays]]

[[Media:Campbell_Heyer_Ch4.pdf | Campbell & Heyer Chapter 4]]

[[Media:Campbell_Heyer_Ch4_figures.pdf | Chapter 4 Color Figures]]
| style="vertical-align: top" | [[Media:20101012_Microarrays.pdf | Introduction to DNA microarray data, Gene Ontology, and GenMAPP/MAPPFinder]]
| style="vertical-align: top; text-align: center" | [[Week 7]]

(due at midnight 10/10; ''Note Different Due Date'')

[[Class Journal Week 7]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right; background: #eee" | Thursday<br/>10/10/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | [http://www.opensource.org/ Open Source]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right" | Tuesday<br/>10/15/2013
| style="vertical-align: top" | [[Media:Ashburner_NatGenet_00_GeneOntology.pdf | Ashburner_NatGenet_00_GeneOntology]]

[[Media:Doniger_GenomeBiology_03_MAPPFinder.pdf | Doniger_GenomeBiology_03_MAPPFinder]]

[[Media:Merrell_Nature_02_vibriomicroarray.pdf | Merrell_Nature_02_vibriomicroarray]]
| style="vertical-align: top" | Journal Club Presentations
| style="vertical-align: top; text-align: center" | [[Week 8]]

(due at midnight 10/18)

[[Class Journal Week 8]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right; background: #eee" | Thursday<br/>10/17/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae DNA Microarray Analysis] activity part 1
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right" | Tuesday<br/>10/22/2013
| style="vertical-align: top" |


| style="vertical-align: top" | [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols DNA Microarray Analysis] activity part 2
| style="vertical-align: top; text-align: center" | [[Week 9]]

(due at midnight 10/25)

[[Class Journal Week 9]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right; background: #eee" | Thursday<br/>10/24/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | 
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right" | Tuesday<br/>10/29/2013
| style="vertical-align: top" |

| style="vertical-align: top" |
* Introduction to XMLPipeDB: export a database

** [[Running GenMAPP Builder]]
* [http://www.opensource.org/ Open Source] review
* Assign groups and species

| style="vertical-align: top; text-align: center" | [[Week 10]]

(due at midnight 11/1)


|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right; background: #eee" | Thursday<br/>10/31/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right" | Tuesday<br/>11/5/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Integrity analysis of Vibrio Gene Database
* [[How Do I Count Thee? Let Me Count The Ways]]
* [[Gene Database Testing Report Sample | Complete your Gene Database Testing Report for ''Vibrio cholerae'']]
| style="vertical-align: top; text-align: center" | [[Week 11]]

(due at midnight 11/8)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right; background: #eee" | Thursday<br/>11/7/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Begin [[Gene_Database_Project | group projects]]
* Select genome paper for journal club
* Select microarray paper in consultation with Dr. Dahlquist
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right" | Tuesday<br/>11/12/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Journal Club Presentations: introduction to my species
| style="vertical-align: top; text-align: center" | [[Week 12]]

(due at midnight 11/15)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right; background: #eee" | Thursday<br/>11/14/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Guild meetings and work session
* Export of Gene Database for your group's species
* Document ID types for your species
* Begin DNA microarray analysis
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right" | Tuesday<br/>11/19/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 13]]

(due at midnight 11/22)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right; background: #eee" | Thursday<br/>11/21/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 14
| style="vertical-align: top; text-align: right" | Tuesday<br/>11/26/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | '''''No Week 14 assignment'''''

|-
| style="vertical-align: top; text-align: center; background: #ded" | 14
| style="vertical-align: top; text-align: right; background: #efe" | Thursday<br/>11/28/2013
| style="vertical-align: top; background: #efe" |
| style="vertical-align: top; background: #efe" | Thanksgiving—no class
| style="vertical-align: top; text-align: center; background: #efe" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right" | Tuesday<br/>12/3/2013
| style="vertical-align: top" |
| style="vertical-align: top; background: #fff" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 15]]

(due at midnight 12/6)
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right; background: #eee" | Thursday<br/>12/5/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #edd" | F
| style="vertical-align: top; text-align: right; background: #fee" | Thursday<br/>12/12/2013
| style="vertical-align: top; background: #fee" |
| style="vertical-align: top; background: #fee" | '''Final project presentations 8:00-10:00 AM'''
| style="vertical-align: top; text-align; background: #fee" |
|-
| style="vertical-align: top; text-align: center; background: #ddd" | F
| style="vertical-align: top; text-align: right; background: #eee" | Friday<br/>12/13/2013 4:30 PM
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | '''Project deliverables due 4:30 PM'''
| style="vertical-align: top; text-align: center; background: #eee" |
|
|}

== Course Information ==

=== Instructors ===

* [[User:Kdahlquist | Kam D. Dahlquist, Ph.D.]]
** http://myweb.lmu.edu/kdahlqui
** Phone: (310) 338-7697
** E-mail: kdahlquist at lmu dot edu
** Office: Seaver 218
** Office hours: Mondays, Tuesdays, and Thursdays 1:30-3:00 PM and by appointment
* [[User:Dondi|John David N. Dionisio, Ph.D.]]
** http://myweb.lmu.edu/dondi
** Phone: (310) 338-5782
** E-mail: dondi at lmu dot edu
** Office: Doolan 106
** Office hours: Tuesdays and Thursdays 11 AM–12 noon, Tuesdays 3–5 PM, and by appointment

=== Prerequisites/Recommended Background ===

To take this course, you must have upper division standing in either the College of Science and Engineering
or the Honors Program. Otherwise, there are no strict prerequisites. Backgrounds in biology and computer science, as well as prior experience with database or information management applications, may be helpful but not necessary.

=== Class Meetings and Attendance ===
TR 9:25 – 10:40 AM, Doolan 219

This is a hands-on, participatory course, thus attendance at all class meetings is required. An unexcused absence from class will result in a 5% deduction from the overall course grade. The instructors should be notified as soon as possible, electronically or by phone, of the reasons for all absences.

Note that the last day to add or drop a class without a grade of W is August 30. The withdrawal or credit/no-credit status deadline is November 1.

=== Mutual Responsibilities ===

This course is designed to foster your development as a biologist and computer scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructors is to provide the expert coaching to support and assist you on your journey. All of the exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

=== Classroom Conduct ===

As an LMU Lion, by the Lion’s Code, you are pledged to join the discourse of the academy with honesty of voice and integrity of scholarship and to show respect for staff, professors, and other students. Refer to [http://studentaffairs.lmu.edu/media/lmustudentaffairs/administration/judicialaffairs/Community%20Standards%20Booklet.pdf LMU’s Community Standards] for the Student Conduct Code or to [http://www.lmu.edu/AssetFactory.aspx?vid=30313 the Lion’s Code]. Disruptive behavior which is persistent or significantly interferes with classroom activities may be subject to disciplinary action. A student may be referred to the Office of Student Judicial Affairs if his or her behavior constitutes a violation of the conduct code. Specifically for this course, the following rules apply:
# You are responsible for your own learning and for being a good class citizen.
# We will act with honesty and integrity at all times.
# We will always treat individuals with respect.
# Class will start promptly on time.
# You are expected to come to class having done the assigned reading and preparatory work.
# You are expected to bring the required materials to each class session.
# Cell phones, pagers, and other communication or music devices must be turned off and put out of sight during class sessions.

=== Course Web Site ===

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/fall2013/. You will need to register  to be able to edit the wiki and complete coursework. Updates to the course schedule and electronic copies of all handouts, assignments, and readings will be posted to this site. You will also use the site to keep an electronic lab notebook/journal for the course. In addition, students have been automatically enrolled in [<add link> BIOL 367-01 on MyLMUConnect]. The MyLMUConnect site may be used for materials that cannot be made public on this wiki, including grades.

=== Required Materials ===

==== Texts ====

There is no required text to purchase for the course; materials will be put on reserve at Hannon Library or will be available online on the this wiki or MyLMUConnect site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* This text has been placed on reserve at the library: Jeffrey Ullman and Jennifer Widom, ''A First Course in Database Systems'', Third Edition. Prentice Hall, 2008.
* Assorted handouts, articles, and sample code will be distributed throughout the semester.
* Additional information is also available on the web; do not hesitate to look for further sources of information regarding the concepts, techniques, tools, and paradigms that we will discuss.

==== Materials (must be brought to each class meeting) ====

* 3-ring binder with all course handouts
* Pen, pencil, extra paper
* USB flash drive to store data
* Keck lab account

=== Course Description ===

The disciplines of biology and computer science come together in bioinformatics, where computational tools are needed to manage and analyze the flood of data coming from new genomics technologies. Biological databases form a significant part of this young and exciting field. This course introduces students to both the biology and computer science expertise needed to understand, use, and develop biological databases. Biology topics include the fundamentals of genetics, molecular biology, and biochemistry needed to understand the data stored in biological databases, as well as the biotechnologies used to gather these data in a high-throughput manner. Computer science topics include what biological databases are, why they are important (and needed), and the challenges that arise in compiling them effectively. Biology and computer science lectures on topics that are relevant to biological databases are coupled with hands-on experience with a variety of software packages ranging from bioinformatics utilities to general-purpose database and software development tools. After learning how to use a biological database, students will be asked to build one of their own.

==== Course Objectives and Learning Outcomes ====

This course is built upon L. Dee Fink’s ''taxonomy of significant learning'', as applied to biological databases. Long after the course concludes, our hope is that:
* You understand how biological information is encoded in the genome and can apply this knowledge to a variety of biological tasks and problems
* You understand the core concepts, structure, and functions of a database, ranging from individual files to a full relational database management system, and can perform useful tasks with such data
* You show discipline and proficiency in day-today science and engineering best practices, such as maintaining journals and notebooks, managing your files and code, and critically evaluating scientific and technical information
* You recognize and care about how the biological and technological issues presented in this course relate to and affect society, our daily lives, and ourselves
* You have some skills and tools for “leaving your comfort zone,” flourishing outside of it, and learning more about biology and computer science on your own
* You learn how to communicate and work effectively with colleagues from different disciplines

=== Course Work and Grading ===

Letter grades are determined as follows: ≥ 90% gets an A– or better; ≥ 80% gets a B– or better; ≥ 70% gets a C– or better. The instructors may curve grades upward based on qualitative considerations such as degree of difficulty, effort, class participation, time constraints, and overall attitude throughout the course. Grades are never curved downward. Current grades will be made available at MyLMU Connect (the system formerly known as Blackboard).

Your work in this course will be assessed in four areas:
{| style="border: 1px dashed rgb(47, 111, 171); background: rgb(249, 249, 249); margin: 1em 0; padding: 1em" cellpadding="5ex"
| Weekly electronic lab notebook/journal assignments (10 points each)
| style="text-align: right" | 140
| points
|-
| Oral presentations
| style="text-align: right" | 90
| points 
|-
| Information literacy
| style="text-align: right" | 45
| points
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 175
| points
|-
| '''Total'''
| style="text-align: right" | '''450'''
| '''points'''
|}


==== Electronic Laboratory Notebook/Journal ====

One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. For computational research, the equivalent of the biology paper-based lab notebook is documentation of your “workflow”. For this course you will practice documentation skills by keeping an electronic lab notebook or journal. The technology we will use is this wiki, that we will create and edit during the semester. You will create an individual user page and make weekly entries that the instructors will read and grade. You will use the wiki to complete the assignments as well. The following guidelines apply:
* Your weekly journal entry is typically due every midnight on Friday PST (''Thursday night/Friday morning''); consult the schedule for specific due dates for each assignment.
* You will earn 10 points per weekly submission. '''''Late journal entries will be accepted up to one week later for up to half credit.'''''
* The instructors will read and comment on how to improve your journal entries.
* Depending on the type of assignment for that week, you may be given the opportunity to make improvements to previous journal entries as the semester progresses.
* Generally, your journal entries will consist of:
** Workflow and other documentation for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Reflection on your learning

==== Oral Presentations ====

You will give four oral presentations in this course. The first three will be in the format of a “Journal Club” presentation where students will present and lead discussion of research articles from the primary literature. The fourth will be a research presentation on your final project. '''''Because that day’s class content is dependent upon each student being ready to present, late oral presentations will not be accepted.'''''

==== Final Group Project ====

* Overall Description of the [[Gene Database Project]], including entire list of deliverables
* [[Gene Database Project Report Guidelines]]

{| style="width: 50%"
| '''Teams'''
| '''Guilds'''
|-
| [[Team1]]
| [[Project Manager]]
|-
| [[Team2]]
| [[GenMAPP User]]
|-
| [[Team3]]
| [[Quality Assurance]]
|-
| [[Team4]]
| [[Coder]]
|}

In addition to the research presentation, the culmination of your final project will be the preparation of a written laboratory report in the style of a manuscript that could be submitted to a peer-reviewed journal. Specific instructions are posted [[Gene Database Project Report Guidelines | here]]. '''''The Final Written Report cannot be accepted any later than Friday, December 13 at 4:30 PM.'''''

==== Work Load Expectations ====
In line with [http://www.lmu.edu/Assets/LMU+Credit+Hour+Policy_Final.pdf LMU’s Credit Hour Policy], the work load expectation for this course is that for every one hour (50 minutes) of classroom instruction, you will complete a minimum of two hours of out-of-class student work each week. This is a 3-unit course with 3 hours (150 minutes) of instruction per week. Thus the expectation is that you will complete 6 hours of work outside of class per week.

==== Extra Credit ====

Students may accumulate up to 2.5% of their final grade in extra credit by attending Department seminars in Biology or Electrical Engineering & Computer Science and completing the seminar sheets. Each seminar attended is worth 0.5% with up to 5 seminars (2.5%) total. You must attend the entire seminar from start to finish and personally turn in your seminar sheet to a faculty member at the end of the seminar.

Certain, non-Biology/Computer Science Department seminars may be approved in advance for extra credit at the instructors’ discretion. To receive credit for these seminars, you must turn in a one-page summary of the seminar '''''within one week''''' of the date of the seminar or they will not count as extra credit.

=== University Policy on Academic Honesty ===

Loyola Marymount University expects high standards of honesty and integrity from all members of its community. All students are expected to follow the LMU honor code. As stated in the LMU Undergraduate Bulletin, “Examples of academic dishonesty include, but are not limited to, the following: all acts of cheating on assignments or examinations, or facilitating other students’ cheating; plagiarism; fabrication of data, including the use of false citations; improper use of non-print media; unauthorized access to computer accounts or files or other privileged information and improper use of Internet sites and resources.” [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm Click here for an online version of the LMU Honor Code and Process].

You are required to sign the Honor Code Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL-CMSI367-HNRS398_HonorCodeAgreement_Fall2013.pdf|Honor Code Agreement]]
* [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm LMU Honor Code and Process, 2013-2014 University Bulletin].
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Guidelines for Literature Citations in a Scientific Paper]]
* [http://www.lmu.edu/Asset388.aspx LRC presentation on plagiarism] (PowerPoint presentation)
* [http://myweb.lmu.edu/dondi/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]

=== Special Accomodations ===

Students with special needs who require reasonable modifications, special assistance, or accommodations in this course should promptly direct their request to the Disability Support Services (DSS) Office. Any student who currently has a documented disability (ADHD, Autism Spectrum Disorder, Learning, Physical, or Psychiatric) needing academic accommodations should contact the DSS Office (Daum Hall 2nd floor, 310-338-4216) as early in the semester as possible. All discussions will remain confidential. Please visit [http://www.lmu.edu/dss www.lmu.edu/dss] for additional information. In addition, please schedule an appointment with the instructors early in the semester to discuss any accommodations for this course for which you have been approved.

=== Revision Notice ===

If necessary, this syllabus and its contents are subject to revision; students are responsible for any changes or modifications announced in class. The most current version of this information resides on this page, the course web site at http://xmlpipedb.cs.lmu.edu/biodb/fall2013/.

== Keck Lab Workstation Guidelines ==

Please visit [[Keck Lab Workstation Guidelines|this page]] for guidelines and instructions on using the Keck computer science lab.

User:Kgosch

2013-09-06T05:11:54Z

Kgosch:

User:Kgosch

2013-09-06T05:11:25Z

Kgosch: added link to week 1 journal entry

Class Journal Week 1

2013-09-06T05:02:08Z

Kgosch: /* Kurt Gosch */ added the "after" answers

Week 1 Reflection Questions:

=='''[[user:Kgosch|Kurt Gosch]]'''==

'''Before'''

''Denning''
#I think of computer science as the study of computational machines. How they function, the theories and history behind their design, and how we can use them to do what we want.
#I believe that the majority of my friends would think it refers primarily to the hardware side of things, as well as just learning a bunch of languages. My older relatives would think of the term computer science as foreign and something "the kids" are doing these days.
#The younger people I know would think it refers to working with the internet and games. Especially anything involving social networking.

''Janovy''
#Biology makes me think of the study of living things. How they grow and reproduce. Also I often associate the term biology with the study of diseases and things in the medical field.
#I would not consider myself a biologist. I think to claim that title would require more direct study of the subject matter, and a better mastery of the material. It would be like a fan of NASCAR calling himself a professional driver (IMO).

'''After'''

#It seems to me that the purpose of the readings is to dispel or clarify any preconceived notions that one might have about what it means to study computer science or what it means to be a biologist.
#It is almost embarrassing to say, but the voice that appeals to me the most is actually the User. I do very much enjoy using all the things that people make. It is my love of using that leads me to want to be a programmer in the first place. The more fun things I make, the more fun things there are to use!
#The principle of Bottlenecks(Evaluation) can apply very easily to my daily life. Not just in the case of living in LA; AKA Trafficlandia, but the case of the piles of clothes in my room. It all needs to make it into my laundry basket, but the only opening in my closet that currently works is rather small. This causes alot of it to spill out and form little hills and valleys for me to adventure through.
#I found it most interesting when he was discussing how early childhood experiences can shape the way we view the world and what fascinates us as adults. A small "insignificant" moment can make huge ripples that shape who we are in the future.
#It means to maintain a curiosity and fascination with the world around us. To view and observe not just the organisms living within it, but also the processes that connect them all to the greater whole. After reading the article I would still not consider myself a biologist on a professional level, but perhaps on a personal one. I do observe the world with a biologists mindset and values. I may not want to study it in detail, but still find nature fascinating and worthy of value. I try to keep and open mind and see the "bigger picture" of life on earth and our place within it. So perhaps in that way I could be considered a biologist.

[[User:Kgosch|Kgosch]] ([[User talk:Kgosch|talk]]) 20:47, 5 September 2013 (PDT)

=='''[[user:mmalefyt|Miles Malefyt]]'''==

Denning pre-questions
#When I hear computer science I think of programming and IT work. Mainly everything having to do with computers
#When older friends hear computer science I'm not exactly sure what they would think of it. It may sound complicated to them
#When my younger friends think of computer science they think of programming and coding
Janovy pre-questions
#When I hear the term Biology the study of life comes to mind. It brings up thoughts of different organisms, how they work, and how they interact with each other
#I consider myself a biologist because I study life and everything having to do with it

could not access the file :(

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 19:23, 5 September 2013 (PDT)

==<div style=" font-size: 200%; line-height: 1.2em">'''[[user:Taur.vil|Tauras]]'''</div>==

Denning Pre-Questions
# When I hear computer science, I think of the underlying processes of the black box I am used to working with. I see computer science as the field of discovering how to create digital processes and then how to improve them.
# I'm not sure, likely the same thing that comes to mind for me but a little more mystery behind it.
# I think they think of it as making computers, but I am not sure.
Janovy Pre-Questions
# When I hear biology, I think of the study of life at all levels from ecosystems down to genetics.
# I do not consider myself purely biologist even though it is the topic of my study. It seems too limited as a lot of my interests are philosophical or psychological although I do use parsimony and evolutionary theory as the governing paradigms in my thought processes.
Post-Reading Questions
# The purpose of these readings was for us to think more deeply about what computer science and biology are.
# The scientist personality appeals to me the most. I'm interested in how the black box works and see the need for future research, but prefer to apply what is being done to questions in the natural world rather than work in the process of discovering or improving technology.
# Hierarchical aggregation applies all throughout biology. Ecosystems are formed by populations, populations by individuals, organisms by cells, cells by organelles. This scaling is pretty much the definition of hierarchical organization which is small fragments that are combined as part of a larger whole.
# I found the most interesting part, and also the part I disagreed with the most, of Janovy's text was that a biologist or a biological mindset is somehow categorically distinct from that of other disciplines. I disagree as his description of the biologist seems to be a general description of an analytical mind and what he seems to separate is mostly the apathetic from the observational. I also disagree with the notion that a biologist has a set of values as well. I don't see how it's necessary to respect or see the wonder of life to study it.
# To be a biologist is to be an inquisitive mind uniquely focused on the natural world. I still cannot consider myself a biologist because my interests expand beyond the area typically considered biology but I am nonetheless biologically minded. I am just interested in additional disciplines as well. (I am aware that this did not change much, that is largely because I disagree with Janovy's defining features of a biologist.)

[[User:Taur.vil|Taur.vil]] ([[User talk:Taur.vil|talk]]) 11:05, 29 August 2013 (PDT)

=='''[[user:vkuehn|Viktoria Kuehn]]'''==

Denning Questions:
# When I hear the term computer science I think of it as an understanding of the way computer programs are made and how they function. It also has to do with applying this knowlegde to other fields and using it efficiently.
# When older relatives hear the term they probably think of the people who created yahoo and the other websites they know how to use.
# I think younger relatives think of it as creating video games.

Janovy Questions:
# When I hear the term Biology I think of it as the study of life, how it functions, and its surroundings.
# I do consider myself a biologist because I am interested in learning and better understanding the way life works.

Reading Questions:
# The purpose of these readings was to introduce the bigger picture of these two areas of study. This clarified any misconceptions and showed their unifying qualities to the readers.
#Surprisingly, the programmer appealed to me the most. I liked the sense of creativity and excitement for the work that was voiced in this section. It presented some qualities that I did not expect to play such an important role in programming.
#The principle of Search/Automation can be applied to many aspects of daily life. People tend to look for connections in life, even if they seem obscure or unrelated. For example, many pieces of art allude to very different ideas than their actual context shows at a first glance. This shows the connections of seemingly unrelated subject matter to give it greater meaning.
#I found his ideas of being a biologist rather than doing biology very interesting. I also found his discussion about one's own values influencing one's career in biology to be very relatable.
#Yes, I consider myself a biologist because I have always had a fascination with how the natural world works and how we fit into it. I also know that this will not cease just because of my future choice of profession.

[[User:Vkuehn|Vkuehn]] ([[User talk:Vkuehn|talk]]) 11:55, 29 August 2013 (PDT)

=='''[[user:kmeilak|Kevin Meilak]]'''==

Before Denning article questions

#Computer science brings to mind people who have learned how to code computers. It is a field that is dedicated to making computers more useful to users.
#It is likely that they think of a complicated system beyond their understanding that some people with a particular aptitude work in but that for most is incomprehensible.
#It is likely that younger friends and relatives think of the many science fiction fantasies that computers can do, such as artificial intelligence.

Before Janovy chapter questions

#Biology brings to mind a field that studies life. It is the scientific approach to what life does and how it works in all of its many forms.
#I consider myself a biologist because I am a biology major. While I do not work full-time in scientific pursuits, I have dedicated this time in my life to the study of life, which is the fundamental aspect of biology. Furthermore, I have engaged in research, which is the quintessential work of a biologist.

After reading questions

#The purpose of these readings was to dispel common misconceptions about both computer science and biology.
#The computational thinker appealed to me the most because of the emphasis on problem solving and because that job links programmers and scientists to do incredible things.
#While it is obvious, and even uses a word created for the human brain before computers and computation, the principle of recollection can be applied to the memory of human brains.
#I found the most interesting and provocative piece of this reading the distinction between identity and action. Someone may work their entire life in a shop, but that does not make them a shopkeeper. And, conversely, there are some people who spend relatively little time in a shop yet consider themselves shopkeepers for nostalgic, idealistic, or other personal reasons. When applied to biology, his critique of the education given to biology majors is valid; they are taught about the science, but not what it means to be a scientist, or why they chose to be one.
#Being a biologist means accepting an identity, typically one that began in fascination with the world. I do consider myself a biologist because of this fascination, and not my chosen major or work. To liken myself to the author’s examples, I had a collection of pine cones, leaves, twigs, dead insects, etc. when I was young because I was fascinated with them. This makes me a biologist far more than any formal education could, for while I do biology, doing something does give an identity.

[https://xmlpipedb.cs.lmu.edu/biodb/fall2013/images/1/10/Databases_journal_article_week_1.pdf Week 1 Journal Entry]

[[User:Kmeilak|Kmeilak]] ([[User talk:Kmeilak|talk]]) 12:11, 29 August 2013 (PDT)

[[Category: Journal Entry]]
[[Category: Shared]]

=='''[[user:kevinmcgee|Kevin McGee]]'''==

Denning Pre-questions
#When I think of computer science, I think of the language and process of imputing a command, and having a computer do that command.
#I feel that many older people have a very limited idea of what computer science is.
#When younger people think of computer science, they probably think of making websites or using social media.
Janovy Pre-Questions
#When I think of Biology, I think of the broad study and observation of life.
#I consider myself a biologist to an extent. This is because while there are many areas of biology that interest me, there is also parts of biology that I am not interested in. Since biology is a broad category, I feel like a cannot consider myself purely a biologist.
Post Reading
#These readings are designed to encourage young students to enter the fields of biology and computer
#Biology spoke to me the most. I am actually very interested in dealing with computers and studying DNA after college.
#An example of a bottleneck is a DUI checkpoint. Police slow down traffic to evaluate whether or not a driver has been drinking.
#I specifically found the part where he talks about post World War II science to be very interesting. He talks about how it brings questions up that we have not had to ask before. This makes me excited for the future of science and where it will take us.
#I do consider myself a biologist. I am, like the Janovy, fascinated with the world around me. I specifically find the aquatic world fascinating. Even if I do not go into this field after college, I know that I will always carry this fascination with the world with me forever.

[[https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/User:Kevinmcgee Kevin McGee]]

[[Category: Journal Entry]]
[[Category: Shared]]

[[User:Kevinmcgee|Kevinmcgee]] ([[User talk:Kevinmcgee|talk]]) 20:11, 3 September 2013 (PDT)

=='''[[User: Gleis| Gabriel Leis]]'''==

'''Denning Pre-questions'''
:#When I hear the term computer science I initially think "uh oh" before recalling my work experience at Hewlett Packard where I learned some basic computer science
:#My parents, upon hearing the words computer science, think deeply before settling their thoughts on their mac computer.
:#When my younger sister hears computer science, I'm sure her first thought is "I hate science and do not understand computers. Ew."
'''Janovy Pre-Questions'''
:#When I hear the term Biology I think immediately about my freshman biology lab.
:#I consider myself a biologist because I frequently wonder about and reflect upon the natural world around me.
'''Post-Reading Questions'''
:#The purpose of these readings is to provide a deeper perspective into the goals of this course. In particular that biology and computer science go hand in hand in the modern science world and are often inseparable in todays research.
:#The voice of the scientist certainly appeals to me most. I find the similarities between computers and living organisms fascinating. I am also very optimistic about the use of computers to advance natural science disciplines in the future.
:#In language, the use of acronyms acts like compression in computing. As a more modern example, texting language is a compressed form of more formal language for the purposes of speed and reduced information volume.
:#The most provocative portion of Janovys writing was his reflection on the interaction of biology and philosophy. Janovy notes that, inevitably, the study of biology leads to the conclusion that the human species is capable of exhausting the natural resources provided by the Earth that may be unreplaceable.
:#According to Janovy a biologist is someone who takes new observations of nature and comes to a greater understanding through these observations. I do not consider myself a biologist because my observations of nature are not novel nor do I feel that I synthesized new understanding of the natural world through my observations.

[[User:Gleis|Gleis]] ([[User talk:Gleis|talk]]) 17:51, 29 August 2013 (PDT)

=='''[[user:HDelgadi|Hilda Delgadillo]]'''==

Before Reading Denning Articles
:1. When I hear the term computer science, I think intricate computer skills and codes, sort of like those in the '' Matrix ''.
:2. When older relatives hear the term computer science, I would think they consider it to be a much harder discipline than it probably really is since they may lack some basic knowledge in regards to computers to being with.
:3. When younger relatives hear the term computer science, I would think they picture video games and fun games in general.

Before Reading Janovy Chapter
:1. When I hear the term Biology, I think of all forms of life on Earth and the life cycle.
:2. I do consider myself a Biologist since I hold a great interest in learning as much information on the inhabitants of this planet and how we proceed to remain on this Earth.

After Reading Denning Articles and Janovy Chapter
:1. I believe the purpose of these readings was to inform the readers how the field of computer science is vastly overlooked. In almost every other field of study, there is always a use for programming and computation. Hence, the field of computer science can be used virtually everywhere, specially in biology.
:2. The voice which was most appealing to me in the '' Voices of Computing '' article was The Programmer. It was interesting to realize how computers would be virtually useless without a program. I never truly realized how programs are significantly emerged into our lives. Programs not only exist in our computers, but also our phones, IPods, cameras, etc. Without programs, the technology around us in our everyday lives would not be as advanced as it is today. Programming drives the advancement of our technology.
:3. A hierarchical aggregation can be applied to getting ready in the morning. In the morning, most people say “I need to get ready", but what does that really entail? It could include fixing ones bed, taking a shower, changing clothes, applying your makeup, fixing your hair, brushing your teeth, etc. This whole process of getting ready in the morning progressively culminates towards the bigger picture, finally being ready to face the day.
:4. One area of the article that I found most interesting was when the author talked about the “conflicting realization” that all biologists encounter that of which humans have made such incredible advancements for this world, but also hold the key and power to destroy the world as quickly as they are proceeding with advancements (Janovy, 2004).
:5. According to Janovy, a biologist must make an original observation in regards to nature. With that observation, conducting research is necessary in order to understand what has been observed. Therefore, I would consider myself a biologist because my curiosity drives me to persist and delve into questions with the purpose of finding answers. I, specially take notice of spider reproductive fitness and its connection with genetics.

[[User: HDelgadi| Hilda Delgadillo]]

=='''[[user:laurmagee|Lauren Magee]]'''==
*Before reading the Denning articles
*# When I hear the word computer science, honestly I think of very challenging coding sequences that make up very useful programs. Computer scientists are those who can translate the foreign language that computers speak into something useful and understandable to the general population.
*# When my elders think about computer science, I don't think they give it much value. They have all grown up in simpler times, where the functions of computers were not a part of their daily life. Therefore the older community, my father especially, believe that computers, and all technology for the matter, are frivolous items to collect.
*#The younger community is very imaginative and has high hopes for the future of computers. They can picture robots doing their chores, cars flying in the air, and toaster's that never leave a slice of bread burnt. There expectations of computer science are limitless and they believe all the wildest inventions of their mind can be brought to life through it.

*Before reading the Janovy chapter
*#When I hear the term biology, I immediately think of genetics. There are other thoughts that run through my mind, 'like cells are the building blocks of life", but because genetics is the main reason I am studying biology, it always comes to the forefront of my mind.
*#I don't consider myself a biologist, because I only concentrate on one factor of biology. The title "biologist", seems to encompass the idea that this individual knows everything that the subject has to offer. I would never strive to be my definition of a biologist, because it is only the study of genetics that I am interested in pursuing.

*After reading the Denning articles and the Janovy chapter
*#The point of these readings was to offer an introduction to and an overview of computer science and biology. The readings provided information on what makes up a biologist or a computer scientists and what types of careers are available in each field.
*#I definitely felt the most connected to the voice of "The Scientist" as I am sure many of my classmates did as well. I want to go into the genetics field, so when the scientist describes discovering new aspects of nature and references DNA, I instantly relate to their position. "The User" also relates to me and my current relationship with computers. I love working on computer, because they aid me a lot in my studies and also provide me with an infinite amount of entertainment. However, I still remain completely oblivious how they function.
*#In my daily life, I do a lot of compressing. I often find myself crunched for time, so I try to learn information in the most efficient way possible. Whether this is reducing my professors lecture into a short page of notes, or writing important information on note cards to study before a test. As for using the exact function of these principles, I think Hierarchical Aggregation can be applied to biology, due to the fact that many times smaller part (i.e. cells) make up a much larger entity (i.e. the human body).
*#I enjoyed the reference to Darwin in the Janovy article, because as I have previously stated many times before, I am interested in genetics. Janovy makes a comparison between Darwin's study environment and current day, noting that very little was known when Darwin was creating his famous ''Origin of a Species'', and there were many religious factors at play that did not support his claim. I think in modern day America, science is no longer second to religion.
*#Janovy classifies a biologist as someone who is inquisitive about the natural world. I would therefore consider myself to be a biologist, due to the fact that I fit within Janovy's definition. However, I don't know many people who don't question the world around them and don't want to know on some level how all the systems encompassed in our environment function.
[[User:Laurmagee|Laurmagee]] ([[User talk:Laurmagee|talk]]) 23:49, 29 August 2013 (PDT)

=='''[[user:Lena|Lena Hunt]]'''==

'''Before Reading the Denning articles:'''
#When I hear the term computer science I think of a bunch of nerds in a dark room doing programming. Programming what? I have no idea. I have been hearing on the news that a Syrian has been shutting down American websites, like the New York Times site. I guess they are computer programmers.
#I don’t think my grandparents would have any idea, they barely know what a computer is. I think my older friends would probably think of hackers, or people who program things for the military, not day to day computer science.
#My younger relatives and friends might have a better idea. Now they are giving laptops to the students at my old high school, so maybe they are learning some computer science and computer science applications.

'''Before reading the Janovy chapter:'''
#When I hear the term biology, I think of ecologists deep in the jungle collecting samples, or of animal behaviorists watching primate interactions. It’s a bit romanticized, but it is what I imagine when I decided I wanted to be a biologist.
#I do consider myself a biologist. Biologists study life, and I am always looking at my surroundings and trying to figure out why plants grow a certain way, or why some animals are more prevalent than others on campus.

'''After reading the Dennings articles and Janovy chapter'''
#The purpose of these readings was to explain what it means to be a computer scientist or biologist, and get people thinking about these fields.
#I guess the scientist's voice appealed to me the most because I am also really excited about discovering things about nature, but all the voices seemed a little far away from my values. I don't know a lot about computers or managing data on computers, and I don't even have a smartphone. Hopefully the voices will resonate with me more after this class.
#Hierarchal Aggregation (Design) can be seen in panels of relief sculpture. The sculptor carved several distinct images, but unless they are all seen together, the panel doesn't make any sense.
#I found it interesting that Janovy made the point that biology is not an isolated field; that it connects everything from history, to art, to sociology.
#I think to be a biologist you have to be in a constant state of wonder with the natural world. That is what drives biologists to keep asking question, and keep searching for answers. I do consider myself a biologist. I am curious about a lot of things, but I think the natural world is the most fascinating and most relevant field of study.

:[[User:Lena|Lena]] ([[User talk:Lena|talk]]) 16:21, 3 September 2013 (PDT)

==[[user:Ksherbina|'''Katrina Sherbina''']]==

'''Before Reading the Denning Articles Questions'''
#When I hear the term ''computer science'', I think of writing, troubleshooting, and implementing code to effectively store and use data.
#I think that when older relatives and friends hear the term ''computer science'' they recall the early computers that took up an entire room, which required punched cards to function.
#When younger relatives and friends hear the term ''computer science'', I think they picture streams of code moving quickly across a monitor as they are being executed.

'''Before Reading the Janovy Chapter Questions'''
#When I hear the term ''biology'', I think of elucidating, particularly through wet lab work, the mechanisms underlying the complex functions and relationships that make life possible.
#I consider myself more of a biomathematician, at least one in training, than a biologist. I am not sure that the term ''biologist'' on its own adequately describes the mix of computational and wet lab work that I have been engaged in during my college career.

'''Post Reading Questions'''
#The purpose of these readings was to dispel the traditional, narrow definitions of biology and computer science. Both the Janovy chapter and the Denning articles discussed how biology and computer science are interdisciplinary pursuits attracting a number of disciplines to work together on various problems.
#On the one hand, I have something in common with the programmer voice due to my acquired love for writing algorithms in R and MATLAB to enable my research. However, I think the scientist voice appeals to me the most because I would not have been able to handle my initial frustration with learning how to write code if I was not doing so to explore genetic regulation.
#The Search principle is applicable to writing papers. In order to produce a coherent written work, it is necessary to pool together various resources and extract a common theme to address.
#What I found most interesting about the Janovy chapter is the notion that it is necessary to consider the roles of an instructor in order to become a good biologist because determining what to teach future generations influences a biologist's decision regarding what to study.
#A biologist observes his or her world actively seeking to uncover the underlying mechanisms of his or her surroundings. In so doing, a biologist interacts with other disciplines and uses a wide array of technology and mathematical tools. From the above definition of a ''biologist'' gleaned from the Janovy reading, I would consider myself a biologist. I think that in my initial answer to this question I got too bogged down in terminology to see the term ''biomathematician'' as one of several terms emerging to describe the new directions branching from the term ''biologist''.

==[[user:mpetredi|'''Mitchell Petredis''']]==
===Denning Articles Pre-Read===
#When I think of computer science, I think of the various types of code that are used to make various programs, from simple scripts to video games.
#I think older relatives view computer science as jargon that’s making life more difficult.
#I think younger relatives and friends mostly see the video game design aspect of computer science.

===Janovy Chapter Pre-Read===
#When I think of biology, I think of the complexity of life and how all the parts come together to make a living thing.
#I consider myself a biologist because it’s what I study and enjoy the most.

===Denning and Janovy Post-Read===
#The purpose of the readings was to better understand the meaning of computer science and biology through the words of professionals
#I’d classify myself mostly as “The User” voice, since I don’t think I’ve done enough to associate myself with “The Computational Thinker” and “The Scientist”. I’ll call myself a hybrid of these three voices.
#The search principle can apply to art in that the computer can identify and filter out specific elements of an artistic piece, such as searching by color, size, style, and kind.
#The most profound thing I saw in the Janovy chapter is how passionate some biologists are about what I would consider mundane subjects, such as the mentioned frog example. Even though its contribution looks weak compared to say the studies of medicine, the fact that these kinds of biologists are happy and satisfied with what they do is admirable to me.
#A biologist, from my interpretation of Janovy’s thoughts, is one who finds the biological world fascinating and continues to ask questions and pursue answers in this field; biologists seek a better understanding of the world around them through natural observations. I still consider myself a biologist from Janovy’s point of view because I think my personality parallels his ideas.
[[User:Mpetredi|Mpetredi]] ([[User talk:Mpetredi|talk]]) 22:06, 29 August 2013 (PDT)Mitchell Petredis

==[[user:Dwilliams|'''Dillon Williams''']]==

Denning Before Questions

#The study of the nature of computers and how to use them in order to further research in technology and theory.
#People who develop computer software and hardware for everyday use.
#People who work in the development of anything involving the use of a computer.

Javoy Before Questions

#The study of living organisms and the way in which they interact within themselves as well as with each other.
#As an aspiring biologist, yes. As a realistic-thinking student who is well aware of the work that professional biologists do on a daily basis, absolutely not.

Post Reading Questions

#To show that both the fields of biology and computer science are far more expansive than most people initially think. The articles helped to dispel any illusion regarding what both subjects are inherently about.
#The computational thinker.
#Hierarchical aggregation can literally be applied to any situation in life. If somebody makes a decision, there are many smaller factors that are effecting the decision as a whole.
#I found the dichotomy that Janovy presented (or at least one that I seemed to notice) fascinating. Throughout the article, Janovy presented the role of the biologist as being somewhat "above" the human capacity based on the assumption that biologists looked at life as part of a system that predated human consciousness. However, after this, Janovy goes on to say that anybody can be a biologist, whether amateur or not, as nature itself is the greatest resource for learning about the study of life.
#After reading Janovy's article, I would say that a biologist is anyone that actively participates in the study of natural phenomena and seeks to understand the motivations and mechanics of these phenomena. In this light, I would consider myself a biologist, as I am always striving to understand more about the natural world around me from both a holistic and atomic point of view.

-[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 23:01, 29 August 2013 (PDT)

==[[user:Ajvree|'''Alina Vreeland''']]==
===Denning Before Questions===
#When I think of computer science, I mostly think of coding, and the process of creating and altering code in order to make a computer run a certain way.
#When others think of computer science, they may think that it involves the creation or innovation of computers. They may also think bout coding, or perhaps the using of computers in science related projects.
#Younger people may think of doing science on a computer, whether it be science research or interactive labs.

===Janovy Before Questions===
#When I hear the term biology, I think of the study of life's processes, and the study of organisms both small and large, and their interactions with each other and the environment.
#I may not be an official biologist in terms of having a job title, but since I am studying biology and interested in biological topics, I think I can considered to be one.

===After Reading Questions===
#All three of the readings strove to break open the meanings of the terms given to the professions of computer scientists and biologists. Each encouraged the reader to reflect on what it meant to actually be involved in each of the fields, and whether or not the terms were more than a professional title. They also seeked to show the similarities between the two fields, and the common misconceptions and myths regarding each of them.
#The voice that appealed to me the most was that of The Scientist. Not only because I am interested in being a scientist myself, but because the idea of discovering new aspects of nature and then being able to apply them to different fields, and vice versa. I'm not as interested in the mathematical and coding aspects, but can appreciate the interconnectedness between it and other areas of science.
#One example of the “Design/Hierarchical Aggregation” principle in biology is the coordination of prganelles to make up a cell, cells to make up a tissue, and tissues to make up an organ.
#The part I found most interesting about Janovy's article is a biologist's ability to see the interconnectedness of observations made in the field and between those of other fields. This is a skill I feel I have not yet mastered, but feel is important for being a successful scientist. The ability to be open-minded and to think critically and openly about what is observed is something I would like to personally improve.
#To be a biologist, one must have a passion for studying elements of nature. It is critical to have this passion whilst engaging in biological study, and not only to have the profession in mind. A biologist looks at the world a certain way, and requires a bit more than technical training. I'd like to think that I have this innate curiousity for nature's elements, and that the technical training I have received is only aiding in my journey to be a successful biologist. However, according to Janovy, a biologist must be able to observe and connect to a wide variety of applications, which I may not be fully attuned to.

[[User:Ajvree|Ajvree]] ([[User talk:Ajvree|talk]]) 23:01, 29 August 2013 (PDT)

==[[user:Slouie|'''Stephen Louie''']]==

Reflection Questions

When I hear the term computer science, I associate it with the study of a computer’s physical and digital design and ways in which programs become applicable in society. For older folks, I believe that they perceive computer science as more of a physical science that deals with computer construction and design. For younger people, I believe they perceive as more of a conceptual science that deals with computer programs and coding.

When I hear the term biology, I think of it as the natural study of biotic and abiotic factors and their interactions within the natural world. I consider myself to be a biologist since my research does concern the study of life in the natural world.

The main purpose of these readings was to shed more light on computer science and biology for those unfamiliar with the subject. In terms of appeal, I would have to say that I am most comfortable with the scientist due to the fact that I very familiar with the description provided by the scientist. An interesting principle of computer science is compression. The human brain is similar to a computer hard drive. As humans develop, data becomes recorded and stored when an unfamiliar situation occurs. Like a computer, the brain can retrieve these memories and use them when a similar situation arises. A particular sentence in the reading that stood out to me was how Janovy said that biology requires an attachment to the world of living things. I see it as statement that says we must recognize that it is important to realize that the purpose of biology is permanently tied to the natural world. Over time, it seems that the term biologist has been converted to a form of an identity to simply a career choice. While I am not currently employed in any major scientific institution or company, I do identify myself as a biologist. As long as I continue to think critically and analytically about the natural world, I believe that it is irrelevant whether I am doing wet work in a lab or presenting my research to a judge.

-[[User:Slouie|Slouie]] ([[User talk:Slouie|talk]]) 00:01, 30 August 2013 (PDT)

Class Journal Week 1

2013-09-06T03:47:03Z

Kgosch: Answered the before questions and added signature

Week 1 Reflection Questions:

=='''[[user:Kgosch|Kurt Gosch]]'''==

'''Before'''

''Denning''
#I think of computer science as the study of computational machines. How they function, the theories and history behind their design, and how we can use them to do what we want.
#I believe that the majority of my friends would think it refers primarily to the hardware side of things, as well as just learning a bunch of languages. My older relatives would think of the term computer science as foreign and something "the kids" are doing these days.
#The younger people I know would think it refers to working with the internet and games. Especially anything involving social networking.

''Janovy''
#Biology makes me think of the study of living things. How they grow and reproduce. Also I often associate the term biology with the study of diseases and things in the medical field.
#I would not consider myself a biologist. I think to claim that title would require more direct study of the subject matter, and a better mastery of the material. It would be like a fan of NASCAR calling himself a professional driver (IMO).

'''After'''

[[User:Kgosch|Kgosch]] ([[User talk:Kgosch|talk]]) 20:47, 5 September 2013 (PDT)

=='''[[user:mmalefyt|Miles Malefyt]]'''==

Denning pre-questions
#When I hear computer science I think of programming and IT work. Mainly everything having to do with computers
#When older friends hear computer science I'm not exactly sure what they would think of it. It may sound complicated to them
#When my younger friends think of computer science they think of programming and coding
Janovy pre-questions
#When I hear the term Biology the study of life comes to mind. It brings up thoughts of different organisms, how they work, and how they interact with each other
#I consider myself a biologist because I study life and everything having to do with it

could not access the file :(

[[User:Mmalefyt|Mmalefyt]] ([[User talk:Mmalefyt|talk]]) 19:23, 5 September 2013 (PDT)

==<div style=" font-size: 200%; line-height: 1.2em">'''[[user:Taur.vil|Tauras]]'''</div>==

Denning Pre-Questions
# When I hear computer science, I think of the underlying processes of the black box I am used to working with. I see computer science as the field of discovering how to create digital processes and then how to improve them.
# I'm not sure, likely the same thing that comes to mind for me but a little more mystery behind it.
# I think they think of it as making computers, but I am not sure.
Janovy Pre-Questions
# When I hear biology, I think of the study of life at all levels from ecosystems down to genetics.
# I do not consider myself purely biologist even though it is the topic of my study. It seems too limited as a lot of my interests are philosophical or psychological although I do use parsimony and evolutionary theory as the governing paradigms in my thought processes.
Post-Reading Questions
# The purpose of these readings was for us to think more deeply about what computer science and biology are.
# The scientist personality appeals to me the most. I'm interested in how the black box works and see the need for future research, but prefer to apply what is being done to questions in the natural world rather than work in the process of discovering or improving technology.
# Hierarchical aggregation applies all throughout biology. Ecosystems are formed by populations, populations by individuals, organisms by cells, cells by organelles. This scaling is pretty much the definition of hierarchical organization which is small fragments that are combined as part of a larger whole.
# I found the most interesting part, and also the part I disagreed with the most, of Janovy's text was that a biologist or a biological mindset is somehow categorically distinct from that of other disciplines. I disagree as his description of the biologist seems to be a general description of an analytical mind and what he seems to separate is mostly the apathetic from the observational. I also disagree with the notion that a biologist has a set of values as well. I don't see how it's necessary to respect or see the wonder of life to study it.
# To be a biologist is to be an inquisitive mind uniquely focused on the natural world. I still cannot consider myself a biologist because my interests expand beyond the area typically considered biology but I am nonetheless biologically minded. I am just interested in additional disciplines as well. (I am aware that this did not change much, that is largely because I disagree with Janovy's defining features of a biologist.)

[[User:Taur.vil|Taur.vil]] ([[User talk:Taur.vil|talk]]) 11:05, 29 August 2013 (PDT)

=='''[[user:vkuehn|Viktoria Kuehn]]'''==

Denning Questions:
# When I hear the term computer science I think of it as an understanding of the way computer programs are made and how they function. It also has to do with applying this knowlegde to other fields and using it efficiently.
# When older relatives hear the term they probably think of the people who created yahoo and the other websites they know how to use.
# I think younger relatives think of it as creating video games.

Janovy Questions:
# When I hear the term Biology I think of it as the study of life, how it functions, and its surroundings.
# I do consider myself a biologist because I am interested in learning and better understanding the way life works.

Reading Questions:
# The purpose of these readings was to introduce the bigger picture of these two areas of study. This clarified any misconceptions and showed their unifying qualities to the readers.
#Surprisingly, the programmer appealed to me the most. I liked the sense of creativity and excitement for the work that was voiced in this section. It presented some qualities that I did not expect to play such an important role in programming.
#The principle of Search/Automation can be applied to many aspects of daily life. People tend to look for connections in life, even if they seem obscure or unrelated. For example, many pieces of art allude to very different ideas than their actual context shows at a first glance. This shows the connections of seemingly unrelated subject matter to give it greater meaning.
#I found his ideas of being a biologist rather than doing biology very interesting. I also found his discussion about one's own values influencing one's career in biology to be very relatable.
#Yes, I consider myself a biologist because I have always had a fascination with how the natural world works and how we fit into it. I also know that this will not cease just because of my future choice of profession.

[[User:Vkuehn|Vkuehn]] ([[User talk:Vkuehn|talk]]) 11:55, 29 August 2013 (PDT)

=='''[[user:kmeilak|Kevin Meilak]]'''==

Before Denning article questions

#Computer science brings to mind people who have learned how to code computers. It is a field that is dedicated to making computers more useful to users.
#It is likely that they think of a complicated system beyond their understanding that some people with a particular aptitude work in but that for most is incomprehensible.
#It is likely that younger friends and relatives think of the many science fiction fantasies that computers can do, such as artificial intelligence.

Before Janovy chapter questions

#Biology brings to mind a field that studies life. It is the scientific approach to what life does and how it works in all of its many forms.
#I consider myself a biologist because I am a biology major. While I do not work full-time in scientific pursuits, I have dedicated this time in my life to the study of life, which is the fundamental aspect of biology. Furthermore, I have engaged in research, which is the quintessential work of a biologist.

After reading questions

#The purpose of these readings was to dispel common misconceptions about both computer science and biology.
#The computational thinker appealed to me the most because of the emphasis on problem solving and because that job links programmers and scientists to do incredible things.
#While it is obvious, and even uses a word created for the human brain before computers and computation, the principle of recollection can be applied to the memory of human brains.
#I found the most interesting and provocative piece of this reading the distinction between identity and action. Someone may work their entire life in a shop, but that does not make them a shopkeeper. And, conversely, there are some people who spend relatively little time in a shop yet consider themselves shopkeepers for nostalgic, idealistic, or other personal reasons. When applied to biology, his critique of the education given to biology majors is valid; they are taught about the science, but not what it means to be a scientist, or why they chose to be one.
#Being a biologist means accepting an identity, typically one that began in fascination with the world. I do consider myself a biologist because of this fascination, and not my chosen major or work. To liken myself to the author’s examples, I had a collection of pine cones, leaves, twigs, dead insects, etc. when I was young because I was fascinated with them. This makes me a biologist far more than any formal education could, for while I do biology, doing something does give an identity.

[https://xmlpipedb.cs.lmu.edu/biodb/fall2013/images/1/10/Databases_journal_article_week_1.pdf Week 1 Journal Entry]

[[User:Kmeilak|Kmeilak]] ([[User talk:Kmeilak|talk]]) 12:11, 29 August 2013 (PDT)

[[Category: Journal Entry]]
[[Category: Shared]]

=='''[[user:kevinmcgee|Kevin McGee]]'''==

Denning Pre-questions
#When I think of computer science, I think of the language and process of imputing a command, and having a computer do that command.
#I feel that many older people have a very limited idea of what computer science is.
#When younger people think of computer science, they probably think of making websites or using social media.
Janovy Pre-Questions
#When I think of Biology, I think of the broad study and observation of life.
#I consider myself a biologist to an extent. This is because while there are many areas of biology that interest me, there is also parts of biology that I am not interested in. Since biology is a broad category, I feel like a cannot consider myself purely a biologist.
Post Reading
#These readings are designed to encourage young students to enter the fields of biology and computer
#Biology spoke to me the most. I am actually very interested in dealing with computers and studying DNA after college.
#An example of a bottleneck is a DUI checkpoint. Police slow down traffic to evaluate whether or not a driver has been drinking.
#I specifically found the part where he talks about post World War II science to be very interesting. He talks about how it brings questions up that we have not had to ask before. This makes me excited for the future of science and where it will take us.
#I do consider myself a biologist. I am, like the Janovy, fascinated with the world around me. I specifically find the aquatic world fascinating. Even if I do not go into this field after college, I know that I will always carry this fascination with the world with me forever.

[[https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/User:Kevinmcgee Kevin McGee]]

[[Category: Journal Entry]]
[[Category: Shared]]

[[User:Kevinmcgee|Kevinmcgee]] ([[User talk:Kevinmcgee|talk]]) 20:11, 3 September 2013 (PDT)

=='''[[User: Gleis| Gabriel Leis]]'''==

'''Denning Pre-questions'''
:#When I hear the term computer science I initially think "uh oh" before recalling my work experience at Hewlett Packard where I learned some basic computer science
:#My parents, upon hearing the words computer science, think deeply before settling their thoughts on their mac computer.
:#When my younger sister hears computer science, I'm sure her first thought is "I hate science and do not understand computers. Ew."
'''Janovy Pre-Questions'''
:#When I hear the term Biology I think immediately about my freshman biology lab.
:#I consider myself a biologist because I frequently wonder about and reflect upon the natural world around me.
'''Post-Reading Questions'''
:#The purpose of these readings is to provide a deeper perspective into the goals of this course. In particular that biology and computer science go hand in hand in the modern science world and are often inseparable in todays research.
:#The voice of the scientist certainly appeals to me most. I find the similarities between computers and living organisms fascinating. I am also very optimistic about the use of computers to advance natural science disciplines in the future.
:#In language, the use of acronyms acts like compression in computing. As a more modern example, texting language is a compressed form of more formal language for the purposes of speed and reduced information volume.
:#The most provocative portion of Janovys writing was his reflection on the interaction of biology and philosophy. Janovy notes that, inevitably, the study of biology leads to the conclusion that the human species is capable of exhausting the natural resources provided by the Earth that may be unreplaceable.
:#According to Janovy a biologist is someone who takes new observations of nature and comes to a greater understanding through these observations. I do not consider myself a biologist because my observations of nature are not novel nor do I feel that I synthesized new understanding of the natural world through my observations.

[[User:Gleis|Gleis]] ([[User talk:Gleis|talk]]) 17:51, 29 August 2013 (PDT)

=='''[[user:HDelgadi|Hilda Delgadillo]]'''==

Before Reading Denning Articles
:1. When I hear the term computer science, I think intricate computer skills and codes, sort of like those in the '' Matrix ''.
:2. When older relatives hear the term computer science, I would think they consider it to be a much harder discipline than it probably really is since they may lack some basic knowledge in regards to computers to being with.
:3. When younger relatives hear the term computer science, I would think they picture video games and fun games in general.

Before Reading Janovy Chapter
:1. When I hear the term Biology, I think of all forms of life on Earth and the life cycle.
:2. I do consider myself a Biologist since I hold a great interest in learning as much information on the inhabitants of this planet and how we proceed to remain on this Earth.

After Reading Denning Articles and Janovy Chapter
:1. I believe the purpose of these readings was to inform the readers how the field of computer science is vastly overlooked. In almost every other field of study, there is always a use for programming and computation. Hence, the field of computer science can be used virtually everywhere, specially in biology.
:2. The voice which was most appealing to me in the '' Voices of Computing '' article was The Programmer. It was interesting to realize how computers would be virtually useless without a program. I never truly realized how programs are significantly emerged into our lives. Programs not only exist in our computers, but also our phones, IPods, cameras, etc. Without programs, the technology around us in our everyday lives would not be as advanced as it is today. Programming drives the advancement of our technology.
:3. A hierarchical aggregation can be applied to getting ready in the morning. In the morning, most people say “I need to get ready", but what does that really entail? It could include fixing ones bed, taking a shower, changing clothes, applying your makeup, fixing your hair, brushing your teeth, etc. This whole process of getting ready in the morning progressively culminates towards the bigger picture, finally being ready to face the day.
:4. One area of the article that I found most interesting was when the author talked about the “conflicting realization” that all biologists encounter that of which humans have made such incredible advancements for this world, but also hold the key and power to destroy the world as quickly as they are proceeding with advancements (Janovy, 2004).
:5. According to Janovy, a biologist must make an original observation in regards to nature. With that observation, conducting research is necessary in order to understand what has been observed. Therefore, I would consider myself a biologist because my curiosity drives me to persist and delve into questions with the purpose of finding answers. I, specially take notice of spider reproductive fitness and its connection with genetics.

[[User: HDelgadi| Hilda Delgadillo]]

=='''[[user:laurmagee|Lauren Magee]]'''==
*Before reading the Denning articles
*# When I hear the word computer science, honestly I think of very challenging coding sequences that make up very useful programs. Computer scientists are those who can translate the foreign language that computers speak into something useful and understandable to the general population.
*# When my elders think about computer science, I don't think they give it much value. They have all grown up in simpler times, where the functions of computers were not a part of their daily life. Therefore the older community, my father especially, believe that computers, and all technology for the matter, are frivolous items to collect.
*#The younger community is very imaginative and has high hopes for the future of computers. They can picture robots doing their chores, cars flying in the air, and toaster's that never leave a slice of bread burnt. There expectations of computer science are limitless and they believe all the wildest inventions of their mind can be brought to life through it.

*Before reading the Janovy chapter
*#When I hear the term biology, I immediately think of genetics. There are other thoughts that run through my mind, 'like cells are the building blocks of life", but because genetics is the main reason I am studying biology, it always comes to the forefront of my mind.
*#I don't consider myself a biologist, because I only concentrate on one factor of biology. The title "biologist", seems to encompass the idea that this individual knows everything that the subject has to offer. I would never strive to be my definition of a biologist, because it is only the study of genetics that I am interested in pursuing.

*After reading the Denning articles and the Janovy chapter
*#The point of these readings was to offer an introduction to and an overview of computer science and biology. The readings provided information on what makes up a biologist or a computer scientists and what types of careers are available in each field.
*#I definitely felt the most connected to the voice of "The Scientist" as I am sure many of my classmates did as well. I want to go into the genetics field, so when the scientist describes discovering new aspects of nature and references DNA, I instantly relate to their position. "The User" also relates to me and my current relationship with computers. I love working on computer, because they aid me a lot in my studies and also provide me with an infinite amount of entertainment. However, I still remain completely oblivious how they function.
*#In my daily life, I do a lot of compressing. I often find myself crunched for time, so I try to learn information in the most efficient way possible. Whether this is reducing my professors lecture into a short page of notes, or writing important information on note cards to study before a test. As for using the exact function of these principles, I think Hierarchical Aggregation can be applied to biology, due to the fact that many times smaller part (i.e. cells) make up a much larger entity (i.e. the human body).
*#I enjoyed the reference to Darwin in the Janovy article, because as I have previously stated many times before, I am interested in genetics. Janovy makes a comparison between Darwin's study environment and current day, noting that very little was known when Darwin was creating his famous ''Origin of a Species'', and there were many religious factors at play that did not support his claim. I think in modern day America, science is no longer second to religion.
*#Janovy classifies a biologist as someone who is inquisitive about the natural world. I would therefore consider myself to be a biologist, due to the fact that I fit within Janovy's definition. However, I don't know many people who don't question the world around them and don't want to know on some level how all the systems encompassed in our environment function.
[[User:Laurmagee|Laurmagee]] ([[User talk:Laurmagee|talk]]) 23:49, 29 August 2013 (PDT)

=='''[[user:Lena|Lena Hunt]]'''==

'''Before Reading the Denning articles:'''
#When I hear the term computer science I think of a bunch of nerds in a dark room doing programming. Programming what? I have no idea. I have been hearing on the news that a Syrian has been shutting down American websites, like the New York Times site. I guess they are computer programmers.
#I don’t think my grandparents would have any idea, they barely know what a computer is. I think my older friends would probably think of hackers, or people who program things for the military, not day to day computer science.
#My younger relatives and friends might have a better idea. Now they are giving laptops to the students at my old high school, so maybe they are learning some computer science and computer science applications.

'''Before reading the Janovy chapter:'''
#When I hear the term biology, I think of ecologists deep in the jungle collecting samples, or of animal behaviorists watching primate interactions. It’s a bit romanticized, but it is what I imagine when I decided I wanted to be a biologist.
#I do consider myself a biologist. Biologists study life, and I am always looking at my surroundings and trying to figure out why plants grow a certain way, or why some animals are more prevalent than others on campus.

'''After reading the Dennings articles and Janovy chapter'''
#The purpose of these readings was to explain what it means to be a computer scientist or biologist, and get people thinking about these fields.
#I guess the scientist's voice appealed to me the most because I am also really excited about discovering things about nature, but all the voices seemed a little far away from my values. I don't know a lot about computers or managing data on computers, and I don't even have a smartphone. Hopefully the voices will resonate with me more after this class.
#Hierarchal Aggregation (Design) can be seen in panels of relief sculpture. The sculptor carved several distinct images, but unless they are all seen together, the panel doesn't make any sense.
#I found it interesting that Janovy made the point that biology is not an isolated field; that it connects everything from history, to art, to sociology.
#I think to be a biologist you have to be in a constant state of wonder with the natural world. That is what drives biologists to keep asking question, and keep searching for answers. I do consider myself a biologist. I am curious about a lot of things, but I think the natural world is the most fascinating and most relevant field of study.

:[[User:Lena|Lena]] ([[User talk:Lena|talk]]) 16:21, 3 September 2013 (PDT)

==[[user:Ksherbina|'''Katrina Sherbina''']]==

'''Before Reading the Denning Articles Questions'''
#When I hear the term ''computer science'', I think of writing, troubleshooting, and implementing code to effectively store and use data.
#I think that when older relatives and friends hear the term ''computer science'' they recall the early computers that took up an entire room, which required punched cards to function.
#When younger relatives and friends hear the term ''computer science'', I think they picture streams of code moving quickly across a monitor as they are being executed.

'''Before Reading the Janovy Chapter Questions'''
#When I hear the term ''biology'', I think of elucidating, particularly through wet lab work, the mechanisms underlying the complex functions and relationships that make life possible.
#I consider myself more of a biomathematician, at least one in training, than a biologist. I am not sure that the term ''biologist'' on its own adequately describes the mix of computational and wet lab work that I have been engaged in during my college career.

'''Post Reading Questions'''
#The purpose of these readings was to dispel the traditional, narrow definitions of biology and computer science. Both the Janovy chapter and the Denning articles discussed how biology and computer science are interdisciplinary pursuits attracting a number of disciplines to work together on various problems.
#On the one hand, I have something in common with the programmer voice due to my acquired love for writing algorithms in R and MATLAB to enable my research. However, I think the scientist voice appeals to me the most because I would not have been able to handle my initial frustration with learning how to write code if I was not doing so to explore genetic regulation.
#The Search principle is applicable to writing papers. In order to produce a coherent written work, it is necessary to pool together various resources and extract a common theme to address.
#What I found most interesting about the Janovy chapter is the notion that it is necessary to consider the roles of an instructor in order to become a good biologist because determining what to teach future generations influences a biologist's decision regarding what to study.
#A biologist observes his or her world actively seeking to uncover the underlying mechanisms of his or her surroundings. In so doing, a biologist interacts with other disciplines and uses a wide array of technology and mathematical tools. From the above definition of a ''biologist'' gleaned from the Janovy reading, I would consider myself a biologist. I think that in my initial answer to this question I got too bogged down in terminology to see the term ''biomathematician'' as one of several terms emerging to describe the new directions branching from the term ''biologist''.

==[[user:mpetredi|'''Mitchell Petredis''']]==
===Denning Articles Pre-Read===
#When I think of computer science, I think of the various types of code that are used to make various programs, from simple scripts to video games.
#I think older relatives view computer science as jargon that’s making life more difficult.
#I think younger relatives and friends mostly see the video game design aspect of computer science.

===Janovy Chapter Pre-Read===
#When I think of biology, I think of the complexity of life and how all the parts come together to make a living thing.
#I consider myself a biologist because it’s what I study and enjoy the most.

===Denning and Janovy Post-Read===
#The purpose of the readings was to better understand the meaning of computer science and biology through the words of professionals
#I’d classify myself mostly as “The User” voice, since I don’t think I’ve done enough to associate myself with “The Computational Thinker” and “The Scientist”. I’ll call myself a hybrid of these three voices.
#The search principle can apply to art in that the computer can identify and filter out specific elements of an artistic piece, such as searching by color, size, style, and kind.
#The most profound thing I saw in the Janovy chapter is how passionate some biologists are about what I would consider mundane subjects, such as the mentioned frog example. Even though its contribution looks weak compared to say the studies of medicine, the fact that these kinds of biologists are happy and satisfied with what they do is admirable to me.
#A biologist, from my interpretation of Janovy’s thoughts, is one who finds the biological world fascinating and continues to ask questions and pursue answers in this field; biologists seek a better understanding of the world around them through natural observations. I still consider myself a biologist from Janovy’s point of view because I think my personality parallels his ideas.
[[User:Mpetredi|Mpetredi]] ([[User talk:Mpetredi|talk]]) 22:06, 29 August 2013 (PDT)Mitchell Petredis

==[[user:Dwilliams|'''Dillon Williams''']]==

Denning Before Questions

#The study of the nature of computers and how to use them in order to further research in technology and theory.
#People who develop computer software and hardware for everyday use.
#People who work in the development of anything involving the use of a computer.

Javoy Before Questions

#The study of living organisms and the way in which they interact within themselves as well as with each other.
#As an aspiring biologist, yes. As a realistic-thinking student who is well aware of the work that professional biologists do on a daily basis, absolutely not.

Post Reading Questions

#To show that both the fields of biology and computer science are far more expansive than most people initially think. The articles helped to dispel any illusion regarding what both subjects are inherently about.
#The computational thinker.
#Hierarchical aggregation can literally be applied to any situation in life. If somebody makes a decision, there are many smaller factors that are effecting the decision as a whole.
#I found the dichotomy that Janovy presented (or at least one that I seemed to notice) fascinating. Throughout the article, Janovy presented the role of the biologist as being somewhat "above" the human capacity based on the assumption that biologists looked at life as part of a system that predated human consciousness. However, after this, Janovy goes on to say that anybody can be a biologist, whether amateur or not, as nature itself is the greatest resource for learning about the study of life.
#After reading Janovy's article, I would say that a biologist is anyone that actively participates in the study of natural phenomena and seeks to understand the motivations and mechanics of these phenomena. In this light, I would consider myself a biologist, as I am always striving to understand more about the natural world around me from both a holistic and atomic point of view.

-[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 23:01, 29 August 2013 (PDT)

==[[user:Ajvree|'''Alina Vreeland''']]==
===Denning Before Questions===
#When I think of computer science, I mostly think of coding, and the process of creating and altering code in order to make a computer run a certain way.
#When others think of computer science, they may think that it involves the creation or innovation of computers. They may also think bout coding, or perhaps the using of computers in science related projects.
#Younger people may think of doing science on a computer, whether it be science research or interactive labs.

===Janovy Before Questions===
#When I hear the term biology, I think of the study of life's processes, and the study of organisms both small and large, and their interactions with each other and the environment.
#I may not be an official biologist in terms of having a job title, but since I am studying biology and interested in biological topics, I think I can considered to be one.

===After Reading Questions===
#All three of the readings strove to break open the meanings of the terms given to the professions of computer scientists and biologists. Each encouraged the reader to reflect on what it meant to actually be involved in each of the fields, and whether or not the terms were more than a professional title. They also seeked to show the similarities between the two fields, and the common misconceptions and myths regarding each of them.
#The voice that appealed to me the most was that of The Scientist. Not only because I am interested in being a scientist myself, but because the idea of discovering new aspects of nature and then being able to apply them to different fields, and vice versa. I'm not as interested in the mathematical and coding aspects, but can appreciate the interconnectedness between it and other areas of science.
#One example of the “Design/Hierarchical Aggregation” principle in biology is the coordination of prganelles to make up a cell, cells to make up a tissue, and tissues to make up an organ.
#The part I found most interesting about Janovy's article is a biologist's ability to see the interconnectedness of observations made in the field and between those of other fields. This is a skill I feel I have not yet mastered, but feel is important for being a successful scientist. The ability to be open-minded and to think critically and openly about what is observed is something I would like to personally improve.
#To be a biologist, one must have a passion for studying elements of nature. It is critical to have this passion whilst engaging in biological study, and not only to have the profession in mind. A biologist looks at the world a certain way, and requires a bit more than technical training. I'd like to think that I have this innate curiousity for nature's elements, and that the technical training I have received is only aiding in my journey to be a successful biologist. However, according to Janovy, a biologist must be able to observe and connect to a wide variety of applications, which I may not be fully attuned to.

[[User:Ajvree|Ajvree]] ([[User talk:Ajvree|talk]]) 23:01, 29 August 2013 (PDT)

==[[user:Slouie|'''Stephen Louie''']]==

Reflection Questions

When I hear the term computer science, I associate it with the study of a computer’s physical and digital design and ways in which programs become applicable in society. For older folks, I believe that they perceive computer science as more of a physical science that deals with computer construction and design. For younger people, I believe they perceive as more of a conceptual science that deals with computer programs and coding.

When I hear the term biology, I think of it as the natural study of biotic and abiotic factors and their interactions within the natural world. I consider myself to be a biologist since my research does concern the study of life in the natural world.

The main purpose of these readings was to shed more light on computer science and biology for those unfamiliar with the subject. In terms of appeal, I would have to say that I am most comfortable with the scientist due to the fact that I very familiar with the description provided by the scientist. An interesting principle of computer science is compression. The human brain is similar to a computer hard drive. As humans develop, data becomes recorded and stored when an unfamiliar situation occurs. Like a computer, the brain can retrieve these memories and use them when a similar situation arises. A particular sentence in the reading that stood out to me was how Janovy said that biology requires an attachment to the world of living things. I see it as statement that says we must recognize that it is important to realize that the purpose of biology is permanently tied to the natural world. Over time, it seems that the term biologist has been converted to a form of an identity to simply a career choice. While I am not currently employed in any major scientific institution or company, I do identify myself as a biologist. As long as I continue to think critically and analytically about the natural world, I believe that it is irrelevant whether I am doing wet work in a lab or presenting my research to a judge.

-[[User:Slouie|Slouie]] ([[User talk:Slouie|talk]]) 00:01, 30 August 2013 (PDT)

User talk:Dondi

2013-09-06T03:20:11Z

Kgosch: finally added my question

*Zerg, Terran, or Protoss? [[User:Kgosch|Kgosch]] ([[User talk:Kgosch|talk]]) 20:20, 5 September 2013 (PDT)

*Outside of designing video games, do you have any other dream jobs? [[User:Kevinmcgee|Kevinmcgee]] ([[User talk:Kevinmcgee|talk]]) 20:20, 3 September 2013 (PDT)

*What advise would you give to someone new to computer science? [[User:Slouie|Slouie]] ([[User talk:Slouie|talk]]) 10:56, 29 August 2013 (PDT)
::Try to find what’s fun or fascinating first. This will help keep you engaged, with an idea of where learning about it can go if you stick with it.
::: — [[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:00, 30 August 2013 (PDT)
*What are some helpful suggestions that will make using wikis less confusing for beginners? [[User:Vkuehn|Vkuehn]] ([[User talk:Vkuehn|talk]]) 11:20, 29 August 2013 (PDT)
::I have two suggestions: first, feel free explore and experiment. The worst that can happen is that things don’t look the way you intended. Otherwise there is really not much to lose. Second, keep looking at other pages’ wiki markup. This will give you lots of examples that you can then use in your own pages.
::: — [[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:00, 30 August 2013 (PDT)
*Have you ever been to Legoland? [[User:Gleis|Gleis]] ([[User talk:Gleis|talk]]) 16:38, 29 August 2013 (PDT)
::Yes—we go almost every year :)
::: — [[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:00, 30 August 2013 (PDT)
*What is your hobby? Hilda Delgadillo: [[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 17:09, 29 August 2013 (PDT)
::I mentioned Lego in class, so that’s one. I also read comic books.
::: — [[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:00, 30 August 2013 (PDT)
*What was the theme of the game you created? [[User:Lena|Lena]] ([[User talk:Lena|talk]]) 17:53, 29 August 2013 (PDT)
::It was called “The Maestro and the Field Marshall.” It tried to be a film noir-themed adventure game. Lots of shades, trench coats, and fedoras :)
::: — [[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:00, 30 August 2013 (PDT)
*Will you ever make another game? [[User:Mpetredi|Mpetredi]] ([[User talk:Mpetredi|talk]]) 19:37, 29 August 2013 (PDT)mpetredi
::I’d sure like to! Maybe when I have bigger blocks of free time on my hands.
::: — [[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:00, 30 August 2013 (PDT)
*What is the most complex project you have ever completed? [[User:Taur.vil|Taur.vil]] ([[User talk:Taur.vil|talk]]) 21:05, 29 August 2013 (PDT)
::I have co-developed an end-to-end health care information system, from scheduling to medical records to billing. Lots of code there.
::: — [[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:00, 30 August 2013 (PDT)
*What interests you the most about biology and why did you decide to get involved with fusing the it with computer science? [[User:Laurmagee|Laurmagee]] ([[User talk:Laurmagee|talk]]) 21:34, 29 August 2013 (PDT)
::My first contact with biology was paleontology—I am very much a dinosaur enthusiast (who isn’t?). Beyond that, I enjoy drawing analogies between biological structures and processes and computational structures and processes; I find the similarities to be striking and fascinating. Sometimes, tantalizing :)
::: — [[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:00, 30 August 2013 (PDT)
*What is the thing that you find most interesting about computer science? - [[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 22:20, 29 August 2013 (PDT)
::I like making things. Knowledge of computer science opens the door to the creation of fun and useful applications, techniques, and other artifacts.
::: — [[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:00, 30 August 2013 (PDT)
*What initially brought you to computer science? [[User:Kmeilak|Kmeilak]] ([[User talk:Kmeilak|talk]]) 23:11, 29 August 2013 (PDT)
::Stereotypical as it may sound, it was games. ’80s computer games started it all. When I started to learn how to program, that put it over the top.
::: — [[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:00, 30 August 2013 (PDT)
*Are there any online resources you would recommend for learning more about computer science? [[User:Ajvree|Ajvree]] ([[User talk:Ajvree|talk]]) 23:23, 29 August 2013 (PDT)
::As a starting point, Wikipedia actually isn’t bad. Aside from that, CodeAcademy works well for learning how to program. Once you have a little programming on you, jsFiddle.net is a great place to practice with immediate results.
::: — [[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:00, 30 August 2013 (PDT)
*Have you considered working solely within the realm of industry rather than academia? [[User:Ksherbina|Ksherbina]] ([[User talk:Ksherbina|talk]]) 23:45, 29 August 2013 (PDT)
::I have, and I did. For a period of around 5 years, I was 100% in industry, working at a tech startup that I cofounded. Good experience, but it had a tendency to get monotonous. I find the rhythms of the academic life, and interactions with students, to be a better fit for me.
::: — [[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:00, 30 August 2013 (PDT)

User talk:Kdahlquist

2013-09-06T03:16:01Z

Kgosch: finally asked my question

*If funding and resources were no issue, what is the one research project you would most want to start/be part of? [[User:Kgosch|Kgosch]] ([[User talk:Kgosch|talk]]) 20:16, 5 September 2013 (PDT)

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*In today's world, what type of projects are being worked on that specifically mix both computer science and biology? [[User:Kevinmcgee|Kevinmcgee]] ([[User talk:Kevinmcgee|talk]]) 20:23, 3 September 2013 (PDT)

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*What is your favorite aspect about this class? [[User:Slouie|Slouie]] ([[User talk:Slouie|talk]]) 10:54, 29 August 2013 (PDT)

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*Have you always been interested in computer science, or are you relatively new to it as well? [[User:Vkuehn|Vkuehn]] ([[User talk:Vkuehn|talk]]) 11:35, 29 August 2013 (PDT)

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*How has your experience with computer science affected your research in biology? [[User:Gleis|Gleis]] ([[User talk:Gleis|talk]]) 16:33, 29 August 2013 (PDT)
** It is ''essential'' to my research in biology. Without the tools of computational biology, I would not be able to analyze the data from the experiments in my lab. You will be learning how to do this analysis as part of the research project in the course. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:02, 5 September 2013 (PDT)''

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*What is a current research project of yours and does it include a computer science aspect to it? Hilda Delgadillo: [[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 17:07, 29 August 2013 (PDT)

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*Do you use computer science/bio informatics in biology disciplines other than molecular or genetic biology? [[User:Lena|Lena]] ([[User talk:Lena|talk]]) 17:51, 29 August 2013 (PDT)

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*What was the best research project that you worked on? [[User:Mpetredi|Mpetredi]] ([[User talk:Mpetredi|talk]]) 19:39, 29 August 2013 (PDT)mpetredi

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* How did you select your research topic? Did you know what you wanted to study going into graduate school? [[User:Taur.vil|Taur.vil]] ([[User talk:Taur.vil|talk]]) 21:03, 29 August 2013 (PDT)
** I'm not sure if you mean my research topic in grad school or now because they have changed. In grad school, I studied the binding of translation initiation factor IF1 to the rRNA of the small subunit A site. I got interested in the ribosome because RNA biology was just coming to the forefront with the discovery of the catalytic activity of RNA. I found my research advisor, Jody Puglisi, after hearing him talk to the grad seminar and after rotating in his lab. For my field, it is customary to rotate in labs so that you can decide which direction you want to go during your first year instead of having to find an advisor when you are applying. I had also considered doing research in plants since I had done that as an undergrad, but ultimately did not find that as interesting as the project I chose. For my postdoctoral work and current work, I wanted to get involved in genomics and bioinformatics because I had always been interested in understanding the cell as an entire system, but until the human genome project, the tools were not available to study all the genes at one time. Now they are and I'm really excited to be in this field. You will be learning about my current research throughout this course. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:16, 5 September 2013 (PDT)''

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*What is one thing you wish you know when you were an undergraduate college student? [[User:Laurmagee|Laurmagee]] ([[User talk:Laurmagee|talk]]) 21:32, 29 August 2013 (PDT)

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*At what point in life did you decide that you wanted to be a biologist? - [[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 22:20, 29 August 2013 (PDT)
*What made you want to be a biologist? [[User:Kmeilak|Kmeilak]] ([[User talk:Kmeilak|talk]]) 23:10, 29 August 2013 (PDT)

** I'll answer Kevin and Dillon's questions together because they are related. My parents got me hooked on science from a young age with things like science camps and books. I remember reading ''Charlie Brown's Big Book of Questions and Answers'' when I was in the primary grades and first learning about cells. My AP Biology class my junior year of high school really cemented my love for biology--I just found everything about cells to be so fascinating. I'm still fascinated by cells and the intricate mechanisms by which they work. I love my job because I get to think about this every day. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:08, 5 September 2013 (PDT)''

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*What helped you decide to collaborate with Dr. Dionisio to create the Biological Databases class? [[User:Ajvree|Ajvree]] ([[User talk:Ajvree|talk]]) 23:19, 29 August 2013 (PDT)

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*Has it been difficult to implement interdisciplinary courses at LMU such as this class? [[User:Ksherbina|Ksherbina]] ([[User talk:Ksherbina|talk]]) 23:47, 29 August 2013 (PDT)
** Dr. Dionisio and I had a relatively easy time when we started team-teaching in Spring 2006. We just had to gain approval from both of our department chairs to teach the first iteration of this class, which was a Master's level class for Computer Science. After the 2008 financial crisis, resources have become more limited and we have been asked to teach this class only every-other-year instead of every year. I imagine that we would have a more difficult time right now getting this class off the ground for the first time. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:35, 4 September 2013 (PDT)''

User:Kgosch

2013-09-06T03:07:37Z

Kgosch: Created page and uploaded general profile info