BOINCSIMAP turns into periodic project

[Desti]

October 12, 2006
BOINCSIMAP turns into periodic project: As to be seen in the project stats and batch monitor, the work for simap and hmmer is limited to few remaining batches. The hmmer calculations went much faster than expected due to the performance optimizations of this application. Thus our databases for protein similarities and domains will soon be up-to-date. We are celebrating this very important milestone and would like to thank all the BOINCSIMAP users that made this happen. Now we will focus on the integration of SIMAP with more bioinformatics methods, portals and databases - thus increasing the impact of out project on computational biology and biosciences. In the future SIMAP will need your contribution by crunching regular updates. Every month updated sequences and domains will be written into simap and hmmer workunits that will need to be calculated. We would be happy if you would stay connected with our project by crunching these periodic batches of work.

[Desti]

Project status
The project has currently no work (see below).
The similarity matrix of the SIMAP project is currently up to date. The calculation of new simap workunits containing the novel proteins from october 2006 will start around november 1st.
The initial calculation of protein domains has been finished. The calculation of updates (new sequences and new domains from InterPro 13.0) will start around november 15th.

[Desti]

November 1, 2006
New workunits: the new workunits for the SIMAP application contain approx. 100.000 new sequences from the databases UNIPROT and GENBANK.

[Desti]

November 30, 2006
New workunits: the approx. 30.000 new workunits for the SIMAP application contain approx. 65.000 new sequences from the databases UNIPROT, RefSeq, PDB and GENBANK. The calculation of these workunits will start in the morning of dezember 2nd. In order to keep the time shorter until the batch of workunits will be calculated we will reduce the report deadline from 10 days to 8 days.

[Desti]

December 15, 2006
New HMMER workunits postponed: due to the release of a new version of the protein domain database InterPro we will adapt our System to InterPro 14.0 first and then start in the middle of january the new HMMER calculations.

[Desti]

January 2, 2007
New workunits: the approx. 70.000 new workunits for the SIMAP application contain approx. 200.000 new sequences from the databases UNIPROT, RefSeq, PDB and GENBANK.

[Desti]

January 15, 2007
New workunits: the approx. 150.000 new workunits for the HMMER application update the domain information in SIMAP to InterPro 14.0. The workunits contain models from the InterPro databases PFAM, PIR, Superfamily, SMART und TIGRFAM.

[Desti]

Project status
Calculation of SIMAP updates is currently running.
The current workunits calculate the similarities and features of the approx. 350.000 new sequences imported during april from the databases Uniprot, RefSeq-Genomes and PDB plus approx. 10.000 new domains from the new InterPro version 15.0.

[Desti]

June 29, 2007
New workunits: The calculation of similarities and features of the approx. 127.000 new sequences, that were imported from the databases PDB, Uniprot and RefSeq in june, will start in the evening of june 30th.

[Desti]

October 1, 2007
New workunits: The calculation of similarities and features of the approx. 85.000 new sequences, that were imported from the databases PDB, RefSeq and Uniprot in september, and the calculation of sequence similarities of several environmental sequencing projects, will start on october 1st in the evening (UTC). To distrubute the workunits more homogeneously, we will test a shorter report deadline of 5 days in combination with a static quota of 100 workunits per cpu and per day.

[Desti]

March 6, 2008
SIMAP upgrade finished: The calculation of about 10 million protein sequences from environmental sequencing projects has been finished. By importing these data, SIMAP has increased its size by a factor of three - from 80 billion stored sequence similarities to more than 250 billion. Thanks to all for chunching millions of workunits during the last months and making this SIMAP upgrade possible by your compute power. SIMAP becomes now a periodic project again, in which we calculate new protein sequences from the relevant datenbases and also new protein sequences from environmental sequencing projects at the beginning of every month.

[Desti]

May 30, 2008
New workunits: The calculation of similarities and features of approx. 180.000 new sequences, that were imported from the databases PDB, RefSeq and Uniprot in may 2008, will start in the evening (UTC) of june 1st.

[Desti]

August 6, 2008
No more workunits in August: The workunits for the preprocessing of the new environmental sequences caused several problems. The most serious issue is that some of the workunits had huge result files that had to be uploaded. For that reason we will not distribute the remaining workunits of this type, but crunch them locally on our servers. The integration of the preprocessed sequences into the main SIMAP database will then be prepared. It will be part of the next batch, starting on September 1st.