Proportal
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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 |
|---|---|---|---|
| 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.
