LncRNA ReleaseNotes

September 8, 2011

Wrong phage genome ID

Phage genome VIMSS IDs don't work (MicrobesOnline IDs), for instance, http://proportal.mit.edu/protein/70464/0/, and select VIMSS.

However,the ones for the cyanobacterial genes work.

Solution:

The VIMSS IDs for proteins are defined in data_dna table, in which many proteins do not have VIMSS ID defined and need to be updated from MicrobesOnline website.

Broken link for data download

The link to Supplementary Data fails: http://proportal.mit.edu/expression/18/, for instance, http://proportal.mit.edu/download/pubmed_17016519/.

Solution:

The supplementary data is available on the Proportal Download page http://proportal.mit.edu/download/, where links for downloading are pointed to a different location, for instance, the link for Nitrogen Availability Gene Expression Project is http://chisholmlab.mit.edu/kat/download/pubmed_17016519/.

Make the following change on templates/gene_express_project.html from,

       Download: <a href="/download/pubmed_Template:Pub.pubmed.pubmed id/">Supplementary Data</a> 

to,

       Download: <a href="http://chisholmlab.mit.edu/kat/download/pubmed_Template:Pub.pubmed.pubmed id/">Supplementary Data</a> 

The supplementary data should be made available directly from Proportal website in next release.

August 16, 2011

EB differentiation time course

An immediate change has been made to ProPortal, the podovirus genome that is identified as P-SSP3 needs to be renamed.This genome was apparently incorrectly named; it is P-SSP5 (also called 9515-10a, which agrees with the currently posted metadata on ProPortal). There is no lysate available for this phage, so perhaps we should also try to figure out if we want it to be on ProPortal at all.

http://proportal.mit.edu/genome/id=58/

We need to get the real P-SSP3 integrated into ProPortal as well. The CAMERA genome annontated as P-SSP3 appears to be correct (according to the cyanophage inventory Excele table P-SSP3 is also named G2087, which agrees with the CAMERA directory name) but while we have FASTA files for it, there's no Genbank file available on the CAMERA FTP site for it. CAMERA has been contacted to get the file:

ftp://ftp.camera.calit2.net/20100928_Prochloro_phage_P_SSP3_G2087/phage/annotation/

Solution:

P-SSP5 has replaced P-SSP3 in data_project table.