GRNsight Gene Page Project Deliverables
From LMU BioDB 2017
| GRNsight Gene Page Project Links | |||||||
|---|---|---|---|---|---|---|---|
| Overview | Deliverables | Reference Format | Guilds | Project Manager | Quality Assurance | Data Analysis | Coder |
| Teams | Page Desiigner | Lights, Camera, InterACTION! | Gene hAPI | JASPAR the Friendly Ghost | |||
Contents
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)
- 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)
- Electronic notebook corresponding to these the microarray results files (Week 8, Week 10, and Weeks 11-15) support reproducible research so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
Grading
- The Group Report is worth 50 points.
- The Group PowerPoint presentation is worth 50 points.
- All other deliverables listed above, together, are worth 50 points.
Group Report
Image of updated outline for Group Report
Qlanners (talk) 15:58, 7 December 2017 (PST)
These guidelines have been modified based on discussion with the Project Managers in class on Thursday, December 7 and shown in the image above.
- 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)
Title Page
Include the following information in a standalone title 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. An abstract is no longer required.
Introduction
The introduction gives the background information necessary to understand your report and should be 3-5 1-2 pages long (double-spaced). The introduction should be in the form of a logical argument that “funnels” from broad to narrow:
- 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.
Combined Materials & Methods/Results/Discussion section
This section will summarize the entire workflow and findings for the project with contributions from all team members, with subsections for the Data Analyst, QA/PM, and Coders. This needs to be a narrative description of what your team actually did, illustrated by figures and tables, as appropriate.
- Optional: 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.
- 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.
Data Analyst
- Table of ANOVA results from the Week 8, discussing the interpretation of the p values.
- From the STEM analyis, include as figures the overall results (the screenshot showing all of the clusters) and then focus on the ones you interpreted for the Week 10 journal assignment.
- Include a table showing the GO results for that cluster (just the narrowed down list of terms that you have interpreted).
- Discuss what the p values for the cluster and for the GO term list mean.
- Discuss the biological interpretation of your GO terms.
- Include a table that lists the transcription factors in your final network and their enrichment p value from YEASTRACT.
- Describe how and why you and your partner chose these transcription factors for your network.
- Include a figure (screenshot) of the unweighted networks visualized with GRNsight.
- Show the GRNsight visualization (screenshot) of the weighted networks, making sure that the genes are placed in the same relative location as each other an as the unweighted network figure.
- Interpret the results of the model as visualized in GRNsight.
Coders
- Give a narrative description of the new features created by the Coders.
- Provide code snippets and/or screenshots to illustrate as necessary.
QA
- Describe the data selected from each database for the gene page and the rationale for its inclusion.
- Describe any other tasks undertaken by the QA.
Conclusions
- Write a 1-2 page conclusion that summarizes the overall project and your findings.
- Overall, what have you learned about the regulation of cold shock in yeast?
- How does the new gene page feature facilitate the data analysis?
- What future directions would you take if you were to continue this project?
- Relate the results of your project to the papers you presented for journal club in Week 11 (Coders) and Week 12 (Data Analyst/QA).
- Did you discover anything new that wasn't reported in the journal club paper (Data Analyst/QA)?
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 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 the APA style that you have been using throughout the semester. Note that the proper format must be followed for both articles and websites, just URLs are not sufficient.
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 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:
- Title slide that gives the main take-home message as the title of your presentation, the authors, date, and venue (course number and title).
- Outline slide that is a summary of take-home messages of your talk (should mirror your conclusion slide)
- The body of your talk (organized in a logical flow, not necessarily in the order given below).
- Introduce the importance/significance of the problem and give background on cold shock in yeast. You can draw from the DA/QA's journal club presentation. This should follow the logic of the Introduction section of your group paper.
- Show a combined flow chart of the tasks/milestones completed by your group (see Materials and Methods of group paper).
- Show the table of ANOVA results.
- Show the screenshot of the overall clustering results and the cluster you focused on .
- Show a table of the GO results from that cluster, giving an interpretation.
- Show the table of regulatory transcription factors in your network and their p values for enrichment.
- Show the unweighted and weighted networks in GRNsight (with the genes arranged in the same way in each figure)
- Explain the new feature for GRNsight created by your team with code snippets and screenshots as appropriate.
- Conclusion slide that mirrors your outline
- Future directions
- Acknowledgments
- References
- 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 | |||||||
|---|---|---|---|---|---|---|---|
| Overview | Deliverables | Reference Format | Guilds | Project Manager | Quality Assurance | Data Analysis | Coder |
| Teams | Page Desiigner | Lights, Camera, InterACTION! | Gene hAPI | JASPAR the Friendly Ghost | |||
