View source for GRNsight Gene Page Project Deliverables

{{GRNsight Gene Page Project Links}}

== Deliverables Checklist ==

* Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
* Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
* Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
* Group PowerPoint presentation (given on Tuesday, December 12, ''.ppt'', ''.pptx'' or ''.pdf'' file)
* Code (GitHub pull request)
** Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the ''original'' GRNsight GitHub repository as a single, unified pull request from the class project’s fork
** Supply a README that summarizes the functionality of your team's new feature (''.txt'' or ''.md'', ''one README per team'')
* Microarray Data Analysis files
** Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
** PowerPoint of screenshots of stem results (''.pptx'')
** Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
** YEASTRACT "rank by TF" results (''.xlsx'')
** GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
** GRNmap output workbook (''.xlsx'')

== Group Report ==

These guidelines are based on the [https://peerj.com/about/author-instructions/ Instructions for Authors] issued by the [https://peerj.com/computer-science/ PeerJ Computer Science] journal. We have made this choice so that, if a group report is considered to be of sufficient quality, we can pursue publication of this report in ''PeerJ Computer Science'' as smoothly as possible. If there are formatting or detail questions that are not covered here, visit the [https://peerj.com/about/author-instructions/ Instructions for Authors] and follow their guidance.

* The report should be written with contributions from all group members.
* Submit as ''.doc'', ''.docx'' or ''.pdf'' file.

=== Style Sheet ===

Use the following guidelines when formatting your report:
* 2.54 cm (1 in) margins on all sides
* Double-spaced
* 12 point Times/Times New Roman font
* Number the pages on the lower-right corner
* Use left justification (“jagged” on the right side)

=== Cover Page ===

Include the following information in a standalone cover page:
* A descriptive title for your project
** The function of the title is to identify the main result or take-home message of the paper. It should be as specific as possible. It can be a phrase or a sentence. What is the main result of your paper that you want to convey with the title?
* The names of the team members (with middle initials)
* The course number and title of the class
* The date of submission

=== Abstract ===

Provide an abstract of no more than 500 words.

=== Introduction ===

The introduction gives the background information necessary to understand your report. The introduction should be in the form of a logical argument that “funnels” from broad to narrow:

<gallery mode="nolines" widths=322px heights=256px>
Funnel.png
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* States importance of the problem
* States what is known about the problem
** Give an overview of what is known about the regulation of the transcriptional response to cold shock in yeast from the Data Analyst/QA's [[Week 12]] journal club article and the information presented by Dr. Dahlquist in class.
** Discuss how you will approach this by analyzing yeast cold shock microarray data from the Dahlquist Lab.
* States what is unknown about the problem
** Which transcription factors belong in the gene regulatory network that controls the cold shock response in yeast is still unknown.
* States clues that suggest how to approach the unknown
** Introduce GRNsight and the GRNsight gene page as the answer to this problem.
* States the question the paper is trying to address
** In this case you want to discover new information about the microarray data using GRNsight.
* State the approach
** Give an overview of your team's contribution to GRNsight and why it is needed.

=== Materials & Methods ===

This section will summarize the entire workflow for the project.  This needs to be a '''''narrative description''''' of what your team actually did, but not a step-by-step protocol.  We are following the standards of reproducible research such that someone else with the appropriate expertise could reproduce what you did given the information in your Materials and Methods section.  You can consider your audience to be the fellow members of your class.

Create a combined flow chart of the tasks/milestones of each of the team members (coders, QA, data analyst) and then describe the flow chart in the text.  You should provide citations to the individual electronic notebooks of the team members as appropriate in the text so that the reader knows where to go for additional details.

=== Results ===

This section will summarize the results of the project.  This section will include figures, tables, and a '''''narrative description''''' of the results shown in those figures and tables.  You should:
* Number each of the figures sequentially and number each of the tables sequentially in order from first mention in the text.  You can either embed your figures and tables in the appropriate place in the text or put them all at the end.  Do not mix both styles, however.
* Write a descriptive legend for each figure and table that briefly states what the figure/table is and gives a brief key to any labels and abbreviations.

=== Discussion ===

{{ Under Construction }}

=== Conclusions ===

Write a concluding paragraph that summarizes the overall project and your findings. 
* How closely do your findings correspond to the original study? 
* Are there significant differences? 
* Did you discover anything new?
* What future directions would you take if you were to continue this project?

=== Acknowledgments ===

Write a short paragraph acknowledging the assistance of anyone who is not a member of your team.

=== References ===

* This section lists all of the references cited in the text of the report (and only those references cited in the paper).  Follow the [[Media:BIOL367_Fall2017_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] handout for general principles.
* Remember that you need to cite anything for which you are not the original source.  Generally, in the introduction, you should aim for a minimum of two in-text citations per paragraph.  You may reference the course web site using the appropriate format for a web reference.
* List your references in alphabetical order by first author using [https://peerj.com/about/author-instructions/#reference-format PeerJ’s recommended reference format]. This format is very similar to APA style and should feel familiar if you have written research papers before.
* To minimize busy work, the PeerJ website includes links to downloadable style files for [https://www.zotero.org/styles/?q=peerj Zotero] and [http://endnote.com/downloads/style/peerj EndNote], if you use either system for managing and rendering references.

== PowerPoint Presentation ==

Each team of students will prepare and give a 20 minute PowerPoint presentation to report the results of their project on Tuesday, December 12 at 2:00-4:00 PM.  
* Please follow the [[Media:PresentationGuidelines.ppt | Presentation Guidelines]] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation) and include the following content:

{{ Under Construction }}

* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by 12:01am, Tuesday, December 12.'''''
** You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructors using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What are the best points about the presentation's organization, visuals, and delivery?  Please give at least 2 specific examples.
*# What points need improvement? Please give at least 2 specific examples.
* We expect that you will take the feedback from your previous presentation into account when doing this presentation.

== Individual Assessment and Reflection ==

Each person on the team will complete an assessment and reflection ''individually''.  If you are comfortable with making this assessment publicly available, you may write it up as a wiki page or as a Word document uploaded to your group deliveables page.  If you prefer to communicate your assessment privately, then email this to both Drs. Dahlquist and Dionisio.

=== Statement of Work ===

* Describe exactly what you did on the project.
* Provide references or links to artifacts of your work, such as:
** Wiki pages
** Other files or documents
** Code or scripts

=== Assessment of Project ===

* Give an objective assessment of the success of your project workflow and teamwork.  
* What worked and what didn't work?  
* What would you do differently if you could do it all over again?
* Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
*# Content: What is the quality of the work? 
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*# Completeness:  Did your team achieve all of the project objectives?  Why or why not?

=== Reflection on the Process ===

* What did you learn?
** With your head (biological or computer science principles)
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
** With your hands (technical skills)?
* What lesson will you take away from this project that you will still use a year from now?

{{GRNsight Gene Page Project Links}}

[[Category:Group Projects]]