WCG@BOINC

[scsimodo]

Human Proteome Folding läuft wieder an:

http://www.worldcommunitygrid.org/forum ... hread=9587

[scsimodo]

WCG startet ein neues Projekt:

http://www.worldcommunitygrid.org/proje ... FgcMain.do

Hmm, ist das nicht genau das, was wir bei SIMAP schon durchexerziert haben? Hier ist es anscheinend statt FASTA der Smith-Waterman-Algorithmus.

[Rincewind]

Dazu steht folgendes im Forum von WCG:

A simple question which needs a simple answer: What's the difference between this project and SIMAP?

Let me ask the same question in a more general setting.

Here is a brief article on BLAST which explains how it replaced the FASTA algorithm due to superior speed: http://www.the-scientist.com/article/display/15682/

Here is some information about PUMA2, a system for High-throughput analysis of (currently 1034) genomes which uses BLAST:
GADU ? Puma2: http://compbio.mcs.anl.gov/
2005 TeraGrid News: http://www.teragrid.org/news/news05/gadu.html
2006 Nucleic Acid Research PUMA2: http://nar.oxfordjournals.org/cgi/conte ... ppl_1/D369

SIMAP ( http://boinc.bio.wzw.tum.de/boincsimap/ ) is described as follows:

What is SIMAP?
SIMAP is a database of protein similarities and protein domains. It contains about all currently published protein sequences and is continuously updated. Protein similarities are computed using the FASTA algorithm which provides optimal speed and sensitivity. Protein domains are calculated using the InterPro methods and databases. SIMAP is to our knowledge the only project that combines comprehensive coverage with respect to all known proteins and incremental update capabilities.


The Fiocruz Genome Comparison Project will produce a database comparing the genes from many genomes with each other using SSEARCH ( http://helix.nih.gov/docs/gcg/ssearch.html ). Here is a brief description I found: SSEARCH - Performs a rigorous Smith-Waterman alignment between a protein sequence and another protein sequence or a protein database, or with DNA sequence to another DNA sequence or a DNA library (very slow).

I notice that each of these projects (Genome Comparison, PUMA2, SIMAP) uses a different algorithm (SSEARCH, BLAST, FASTA). What other similarities and differences do they have?

(Please note - I'm not complaining. I think that important scientific work ought to be done using many different methods to discover as much as possible and catch errors.)

Added: For the benefit of people reading this thread who are trying to learn more, I will post the URL for the Genome Comparison project description: http://www.dbbm.fiocruz.br/GenomeComparison

It begins:

The Genome Comparison Project: Improving protein functional annotation in databases

Over the years, a rather large body of secondary information (structural, functional, similarities to other entries and a variety of cross-references) has been attached to protein database entries. Once such information is entered, it rarely gets updated or corrected. Thus, annotation of predicted protein function is often incomplete, uses non-standardized nomenclature or can be incorrect when inferred from previous, incorrectly annotated sequences. Additionally, many proteins are composed of several structural and/or functional domains (modules comprising distinct evolutionary, functional and structural units), which can be overlooked by automated annotation procedures. Moreover, the comparative information available today is huge when compared to the early days of genomics.

The main objective of the Genome Comparison Project is to perform a complete pairwise comparison between all predicted protein sequences, obtaining similarity indices that will be used, together with standardized Gene Ontology (http://www.geneontology.org), as a reference repository for the annotator community, providing an invaluable data source for biologists. The sequence similarity comparison program used in the Genome Comparison Project is called SSEARCH (W.R. Pearson [1991] Genomics 11:635-650), a freely available implementation of the Smith-Waterman rigorous algorithm (T. F. Smith and M. S. Waterman [1981] J. Mol. Biol. 147:195-197) (algorithm is an organized procedure for performing a given type of calculation or solving a given type of problem), which finds the mathematically best local alignment between pairs of sequences.

As a result, precise annotation, correction of inconsistencies, and assignment of possible functions to hypothetical proteins of unknown function will be possible. Moreover, proteins with multiple domains and functional elements will be correctly spotted. Even distant relationships will be detected.


Added even later: I have been thinking about Genome Comparison and SIMAP. Instead of just waiting for an answer, I'll throw out my most recent idea for public display.

( angel I must like to hear myself talk. I must have been insufferable back in the third grade. nerd Come to think of it, I remember being surprised back in high school when I could not convince a schoolmate that there were no flying saucers and gave up the argument. One of the bystanders exclaimed that it was great to finally see me lose an argument. I had not thought of my arguing in that sort of way. After all - - I was always right! laughing Just insufficiently persuasive some times. Ummm. . . . Perhaps I achieved my present state of perfection more slowly than I like to think. tired )

SIMAP compares proteins and Genome Comparison compares genes. Although there is a very close relationship between genes and the proteins that they code for, it is not a direct one-to-one relationship. The genetic code ( http://en.wikipedia.org/wiki/Genetic_code ) has several alternative ways to code for each amino acid in a protein. Even worse, there are some species that have modified the genetic code so that they produce non-standard amino acids in response to a genetic sequence. Just looking at the protein that is produced from a gene loses a lot of information that is present in the gene. So evolutionary relationships should be tracked using genes as the Fiocruz Genome Comparison project does rather than by using proteins from SIMAP. The functions performed by a protein are more likely to be the same in different organisms if they are closely related rather than distantly related.

This must seem obvious to anyone in the biological sciences. But I studied math and physics. smile

EDIT:
Und hier auch noch der Link zu dem Thema.

[Michael H.W. Weber]

Ja, ich hab' die erste WU vom neuen Projekt schon bekommen. Hängt noch in der Warteschleife...

Michael.

[scsimodo]

Ja, ich hab' die erste WU vom neuen Projekt schon bekommen. Hängt noch in der Warteschleife...

Michael.

Hmm..., ich bekomme andauernd folgende Meldung:

2006-11-19 16:05:40 [World Community Grid] Message from server: Project encountered internal error: shared memory
2006-11-19 16:05:40 [World Community Grid] Project is down

[Michael H.W. Weber]

Meine WU kam bereits vorgestern...

Michael.

[tomXYZ]

Ich bekomme auch "project is down" Meldungen. Ich nehme an, sie arbeiten daran:
https://secure.worldcommunitygrid.org/f ... 9967#77506
Etwas ähnliches ist vor ein paar Wochen schon mal passiert und wurde nach kurzer Zeit behoben:
https://secure.worldcommunitygrid.org/f ... 2&offset=0
http://www.worldcommunitygrid.org/forum ... hread=8806

[Rincewind]

Hey Leute, steckt eure Resourcen lieber in QMC *g*

EDIT:
Also, nach dem die Diskussion ja hierher verlegt werden soll:

Wow, you seem unhappy.

Meint er das ernst?

Ist aber wirklich sehr interessant.
Vor allem da anscheinend dort der Cluster als unökonomisch angesehen wird. Wenn jetzt mal aus Spaß alle Teams ihre Cluster bzw. Rechnerfarmen von WCG abziehen würden, hätten die Jungs dort ein ganz extremen Einbruch.

Als Beleg die offiziele Rangliste der Member, nach Results geordnet.

http://www.worldcommunitygrid.org/stat/ ... rt=results

Interessant ist, dass z.B. der 50 innerhalb von ziemlich genau 2 Jahren ca. 35,5 Jahre Rechenleistung erbracht hat. Was also so ca. 17-18 24/7 Rechner ausmachen würde. Und das ist meiner Meinung nach KEIN normaler Computer benutzer von denen in der Antwort die Rede ist.

[Uwe Sänger Herzke]

Ich hab's gerade dort im Forum angefragt, mal schaun, was sich da demnächst tut.

[Dennis Kautz]

WCG@BOINC ist derzeit nicht erreichbar, der UD-Client tut aber noch. Anscheinend tobt dort über'm Teich ein Blizzard. Schade eigentlich, ich finde, WCG wird langsam aber sicher immer interessanter

EDIT: Doch n Festplattenfehler wurde mir grad mitgeteilt. Die Fehlerbehebung kann wohl bis zu 72h dauern.

[Dennis Kautz]

Und geht wieder...

[Dennis Kautz]

Nicht schlecht, was ein gewisser Garfield bei uns im Team so abliefert

Falls Du das hier liest, Garfield: Darf man fragen, was du an Maschinchen im Einsatz hast?