Difference between revisions of "Week 10"
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=== Annotated Bibliography of Genomics Papers for your Species === | === Annotated Bibliography of Genomics Papers for your Species === | ||
| − | * | + | For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species. Glenn Johnson-Grau will be giving a guest presentation in class on Tuesday, October 29 to introduce you to searching various bibliographic databases. |
| − | * | + | |
| − | * | + | * On your individual journal entry pages, you will keep an electronic lab notebook that details how you conducted your search, along with the results of your search. |
| − | * | + | ** For each search you perform, state which database you used (e.g., GoogleScholar, PubMed, ISI Web of Science/Knowledge). |
| − | * | + | ** State what you used as search terms and what type of search terms ( |
| − | * | + | * On your team page (see shared assignment below), you will combine your results with your teammates into one final, ranked bibliography. Specifically, you need to search the literature/biological databases for the following: |
| − | * | + | *# The journal article which describes the results of the whole genome sequencing for your species. |
| − | * | + | *#* Create a link to the HTML version of your journal article on the publisher web site. ''Note that PubMed Central is not an actual publisher web site, but a secondary database of papers.'' |
| − | * | + | *#* Download the PDF file of the journal article, upload it to the wiki and link to it from your team's home page. ''Note that you can only upload the PDF file to our wiki if there are no copyright restrictions on the article. If there are copyright restrictions, then you will need to provide a link to the download on the publisher site.'' |
| − | * | + | *# Five to ten potential journal articles that refer to public microarray data for your species. The instructors will evaluate the suitability of the data for each of the articles for the final project and one will be chosen next week to pursue. |
| − | * | + | *#* The experiments must be measuring '''''gene expression''''' aka '''''transcriptional profiling'''''. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis. |
| − | * | + | *#* You must find both the journal article (link to the article web page and also download and post the PDF) and the microarray data (link to the web site; download and post the dataset). It will probably be easier to find the microarray data first and then find the corresponding journal article. |
| − | * | + | *#* Remeber, microarray data is not centrally located on the web. Some major sources are: |
| + | *#** [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO] | ||
| + | *#** [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress] | ||
| + | *#** [http://smd.stanford.edu/ Stanford Microarray Database] | ||
| + | *#** [http://puma.princeton.edu/ PUMAdb (Princeton Microarray Database)] | ||
| + | *#** In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site. | ||
== Team Journal Assignment == | == Team Journal Assignment == | ||
Revision as of 20:15, 17 October 2013
Under Construction
The content in this page has not been finalized and is still subject to change. Use the current information at your own risk.
This journal entry is due on Friday, November 1, at midnight PST. (Thursday night/Friday morning)
Individual Journal Assignment
- Store this journal entry as "username Week 10" (i.e., this is the text to place between the square brackets when you link to this page).
- Link from your user page to this Assignment page.
- Link to your journal entry from your user page.
- Link back from your journal entry to your user page.
- Don't forget to add the "Journal Entry" category to the end of your wiki page.
- Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.
Annotated Bibliography of Genomics Papers for your Species
For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species. Glenn Johnson-Grau will be giving a guest presentation in class on Tuesday, October 29 to introduce you to searching various bibliographic databases.
- On your individual journal entry pages, you will keep an electronic lab notebook that details how you conducted your search, along with the results of your search.
- For each search you perform, state which database you used (e.g., GoogleScholar, PubMed, ISI Web of Science/Knowledge).
- State what you used as search terms and what type of search terms (
- On your team page (see shared assignment below), you will combine your results with your teammates into one final, ranked bibliography. Specifically, you need to search the literature/biological databases for the following:
- The journal article which describes the results of the whole genome sequencing for your species.
- Create a link to the HTML version of your journal article on the publisher web site. Note that PubMed Central is not an actual publisher web site, but a secondary database of papers.
- Download the PDF file of the journal article, upload it to the wiki and link to it from your team's home page. Note that you can only upload the PDF file to our wiki if there are no copyright restrictions on the article. If there are copyright restrictions, then you will need to provide a link to the download on the publisher site.
- Five to ten potential journal articles that refer to public microarray data for your species. The instructors will evaluate the suitability of the data for each of the articles for the final project and one will be chosen next week to pursue.
- The experiments must be measuring gene expression aka transcriptional profiling. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
- You must find both the journal article (link to the article web page and also download and post the PDF) and the microarray data (link to the web site; download and post the dataset). It will probably be easier to find the microarray data first and then find the corresponding journal article.
- Remeber, microarray data is not centrally located on the web. Some major sources are:
- NCBI GEO
- EBI ArrayExpress
- Stanford Microarray Database
- PUMAdb (Princeton Microarray Database)
- In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
- The journal article which describes the results of the whole genome sequencing for your species.
Team Journal Assignment
Team Membership
To be determined.
Creating a Team Wiki Page
From this week on, your "Shared Journal Assignments" will become "Team Journal Assignments". For this week, some preliminary tasks are assigned to your team in preparation for the launch of the final projects.
- Name your team and create your team home page on the wiki.
- The name of your team home page should simply be the team name.
- This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to communicate with each other and with the instructors. Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.
- Create a link to your team's page on the course Main page.
