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# [http://proportal.mit.edu/ '''ProPortal'''] Prochlorococcus Portal is a web analytical tool for Prochlorococcus, a model system for Integrative Systems Biology.
{{BioMicroCenter}}
 
[http://proportal.mit.edu/ '''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=
=References=
*[https://wikis.mit.edu/confluence/display/CHISHOLMLAB/Bioinformatics '''Chisholm Lab Bioinformatics Wiki''']
*[http://cyano2.mit.edu/mediawiki/index.php?title=Main_Page Proportal Wiki]


=Project Timelines=
*[http://cyano2.mit.edu/mediawiki/index.php?title=Main_Page '''Proportal Wiki''']
*[https://wikis.mit.edu/confluence/display/CHISHOLMLAB/Bioinformatics '''Chisholm Lab Bioinformatics Wiki''']: You need login to get access.
*[http://www.broadinstitute.org/annotation/viral/Phage/Home.html '''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 [[Proportal_Project_2011 | Year 2011]].
 
{| class="wikitable" style="width:90%" border="1"
{| class="wikitable" style="width:90%" border="1"
|+Schedule
|+Schedule
Line 11: Line 19:
! Timelines !! Plan !! Status !! Comments
! Timelines !! Plan !! Status !! Comments
|-
|-
! Jul 22, 2011
! August 31, 2012
| 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_DBSchema | 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
| Paper for RNA-seq data analysis || Finalize the data analysis.
|| Add your comments
|-
|-
! Jul 29, 2011
! August 31, 2012
| 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 [[Proportal_ReleaseNotes |Release Notes]] for a number of issues resolved. || Add your comments
| Proportal || Single cell genomes, links for the RNA-seq and microarray data are to be added to Proportal
|| Add your comments
|-
|-
! Aug 5, 2011
! July 31, 2012
| Modification of cluster analysis using static/manual processing. || Refer to the [[Proportal_ReleaseNotes |Release Notes]] for a number of issues resolved. || Add your comments
| COG pipeline || 96 partial genomes from BATS and 19 from HOT (115 in total) are to be processed.
|| Add your comments
|-
|-
! Aug 15, 2011
! June 31, 2012
| Due date for submitting the database paper || Refer to the [[Proportal_ToDoList | 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
| Paper for overlapped genes in both host and phage genomes || Review the manuscript and prepare the latest version of COG clusters with overlapped genes.
|| 33 new genomes have been processed using the modified COG pipeline. The paper will be based on the final version of COG clusters for shared phage/host genes.
|-
|-
! Aug 31, 2011
! June 31, 2012
| The GIT repository for version control and the wiki server for Proportal helps, user feedback, and data uploading etc. || Refer to the [[Proportal_ReleaseNotes |Release Notes]] for a number of issues resolved. || Add your comments
| assemblies for HL III/IV single cell || Access biome.mit.edu and add them to the ProPortal.
|| GenBank files have been prepared for the submission of Rex's paper.
|-
! June 15, 2012
| COG cluster pipeline. || Modify the script for uploading genomes with multiple contigs, which was missing in the current pipeline.
|| The bug in the COG pipeline has been fixed for processing genomes with multiple contigs and undefined unique protein identifiers.
|-
! 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.
|| The RNA-Seq pipeline is working as expected using BWA/DESeq/GSEA. Genome functional annotations have been investigated. A better set of parameters in Cufflinks is to be determined for Prochlorococcus genome. 
|-
! February 28, 2012
| Run COG cluster pipeline on new genomes. || The COG cluster pipeline is applied to both host and phage genomes.
|| The current version of the COG scripts does not work well for genomes that have multiple contigs or whose unique protein identifiers are not defined yet.
|-
|-
! Oct 31, 2011
| Automation of cluster analysis using dynamic processing and network visualization. || Refer to the [[Proportal_ReleaseNotes |Release Notes]] for a number of issues resolved. || Add your comments
|}
|}
=To-do List=
For the detail of current issues that have been identified, refer to the [[Proportal_ToDoList | To-do List]].


=Proportal DB Schema=
=Proportal DB Schema=
Line 36: Line 62:
Some issues in the current version of Proportal have been resolved. Refer to the [[Proportal_ReleaseNotes |Release Notes]] for more details.
Some issues in the current version of Proportal have been resolved. Refer to the [[Proportal_ReleaseNotes |Release Notes]] for more details.


=[[Proportal_ToDoList | To-do List]]=
=Strain Discussion=
This section is devoted to the discussion on issues related to [[Proportal_Strains | various strains]] stored in Proportal DB.
 
=Frequently Asked Questions=
This section provides answers to some [[Proportal_FAQs | frequently asked questions]].

Latest revision as of 08:09, 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

Project Management

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

Schedule
Timelines Plan Status Comments
August 31, 2012 Paper for RNA-seq data analysis Finalize the data analysis. Add your comments
August 31, 2012 Proportal Single cell genomes, links for the RNA-seq and microarray data are to be added to Proportal Add your comments
July 31, 2012 COG pipeline 96 partial genomes from BATS and 19 from HOT (115 in total) are to be processed. 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. 33 new genomes have been processed using the modified COG pipeline. The paper will be based on the final version of COG clusters for shared phage/host genes.
June 31, 2012 assemblies for HL III/IV single cell Access biome.mit.edu and add them to the ProPortal. GenBank files have been prepared for the submission of Rex's paper.
June 15, 2012 COG cluster pipeline. Modify the script for uploading genomes with multiple contigs, which was missing in the current pipeline. The bug in the COG pipeline has been fixed for processing genomes with multiple contigs and undefined unique protein identifiers.
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. The RNA-Seq pipeline is working as expected using BWA/DESeq/GSEA. Genome functional annotations have been investigated. A better set of parameters in Cufflinks is to be determined for Prochlorococcus genome.
February 28, 2012 Run COG cluster pipeline on new genomes. The COG cluster pipeline is applied to both host and phage genomes. The current version of the COG scripts does not work well for genomes that have multiple contigs or whose unique protein identifiers are not defined yet.

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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