Proportal

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(Project Management)
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Revision as of 09:39, 9 July 2012

Image:BioMicroCenter-header6.jpg

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.

Contents

References

Project Management

For the project management in previous years, refer to year 2011.

Schedule
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.

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