Proportal: Difference between revisions
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=Project Management= | =Project Management= | ||
For the project management in previous years, refer to [[Proportal_project2011 | year 2011]]. | |||
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Revision as of 07:39, 9 July 2012
| HOME -- | SEQUENCING -- | LIBRARY PREP -- | HIGH-THROUGHPUT -- | COMPUTING -- | OTHER TECHNOLOGY |
ProPortal Prochlorococcus Portal is a web analytical tool for Prochlorococcus, a model system for Integrative Systems Biology.
The information provided here is for the general purpose of user contribution and especially collaboration. While the lab members may have access to their internal secure wiki's, however, people will benefit from sharing the information and maintaining a collaborative environment for sustainable development.
References
- Proportal Wiki
- Chisholm Lab Bioinformatics Wiki: You need login to get access.
- Marine Phage, Viruses and Viromes The Gordon & Betty Moore Foundation's Marine Microbiology Initiative (MMI) at Broad institute.
Project Management
For the project management in previous years, refer to year 2011.
| Timelines | Plan | Status | Comments |
|---|---|---|---|
| July 31, 2012 | Paper for RNA-seq data analysis | Finalize the data analysis. | Add your comments |
| June 31, 2012 | Paper for overlapped genes in both host and phage genomes | Review the manuscript and prepare the latest version of COG clusters with overlapped genes. | Add your comments |
| June 31, 2012 | assemblies for HL III/IV single cell | Access biome.mit.edu and add them to the ProPortal. | Add your comments |
| June 15, 2012 | COG cluster pipeline. | Modify the script for uploading genomes with multiple contigs, which was missing in the current pipeline. | Add your comments |
| May 31, 2012 | RNA-Seq processing and analysis pipeline. | Verify RNA-Seq processing pipeline. Prepare genome annotations. Run downstream analysis on phage infection RNA-Seq data. | Add your comments |
| February 28, 2012 | Run COG cluster pipeline on new genomes. | The COG cluster pipeline is applied to both host and phage genomes. | Add your comments |
| Dec 31, 2011 | Finish COG cluster pipeline. | Finally, the COG cluster pipeline is working for new genomes added into Proportal development database. | Add your comments |
| Dec 31, 2011 | Finish COG cluster pipeline. | Finally, the COG cluster pipeline is working for new genomes added into Proportal development database. | Add your comments |
| Nov 21, 2011 | The Proportal paper is out. | Full Text: http://nar.oxfordjournals.org/cgi/content/full/gkr1022 | Add your comments |
| Oct 31, 2011 | Automation of cluster analysis using dynamic processing and network visualization. | Refer to the Release Notes for a number of issues resolved. | Add your comments |
| Aug 31, 2011 | The GIT repository for version control and the wiki server for Proportal helps, user feedback, and data uploading etc. | Refer to the Release Notes for a number of issues resolved. | Add your comments |
| Aug 15, 2011 | Due date for submitting the database paper | Refer to the To-do List for a number of issues that should be addressed before the submission. Finally, the manuscirpt was submitted on time! | Add your comments |
| Aug 5, 2011 | Modification of cluster analysis using static/manual processing. | Refer to the Release Notes for a number of issues resolved. | Add your comments |
| Jul 29, 2011 | Update of datasets in Proportal public website. Migrate/merge all datasets stored in the development and production databases. Verify the integrity and consistency between the development and production databases and websites. | Refer to the Release Notes for a number of issues resolved. | Add your comments |
| Jul 22, 2011 | Modification of Proportal DB Schema. Re-create all tables in a new database with all the missing foreign keys and their cascade properties. | The new Proportal DB Schema has been created by adding all missing foreign keys in the current version. A number of errors are to be fixed in next week to synchronize the datasets stored in the development and production databases. | Add your comments |
To-do List
For the detail of current issues that have been identified, refer to the To-do List.
Proportal DB Schema
The new Proportal DB Schema is created by adding all the missing foreign keys back into the database. Some orphan records have been identified from this process and will be fixed/removed from next release of Proportal.
Release Notes
Some issues in the current version of Proportal have been resolved. Refer to the Release Notes for more details.
Strain Discussion
This section is devoted to the discussion on issues related to various strains stored in Proportal DB.
Frequently Asked Questions
This section provides answers to some frequently asked questions.
