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WCG Status Update

WCG Post

HPF2 Update - January 2011

Greetings WCG Community,

Happy new year! I have taken it upon myself to write a quick status update regarding the Human Proteome Folding project, in part to introduce myself and also to summarize a few of the tasks that lie ahead for us.

As of early January, the Bonneau lab team working on the HPF project has undergone a slight change of staff. Patrick Winters, from whom you have heard in previous updates, has moved on to other pastures, and I have taken his place. My name is Duncan Penfold-Brown, and I am coming out of a previous research position in the application of high-powered computing (both Grid and Cloud) to high-energy physics and astronomy. I have a degree in computer science, and have in the past focused on distributed and self-organizing systems. I also have experience (and a great deal of interest) in bioinformatics, which I look forward to increasing in my work on this project.

In short, I will be responsible for support and development of HPF projects and research. I am interested in pursuing a greater knowledge of proteomics - which seems to me like biological puzzle solving - and also the applications (medical, investigative) of the research we are completing together.

The immediate tasks we are approaching are to work on improving our pre- and post-analysis tools, in order to get more data to the Grid, and to better interpret what comes out. Goals for the immediate future include continuing the incorporation of phylogenetic data and evolutionary analysis of protein domains into our analysis process in order to enhance our annotation of select unknown proteins. This incorporation will provide us with a better understanding of the function of unknown proteins, as we can more accurately identify evolutionarily similar structures and cross-examine their structure-function relationships. With additions to our analysis process and continued work, we will ultimately be improving the end data of our research.

Speaking of data, here is a quick update of what is currently being turned over on the WCG:

Currently, all protein data being folded is from the Human Microbiome Project (HMP - see their site at http://commonfund.nih.gov/hmp/), with a focus on microbes found in the human gut. As of late January, we have completed pre-analysis on the last of the data that we will be working on from the HMP (for now), and have dropped it off to be picked up by the grid (see codes 'oh' - 'ok' in the following table).

We are now looking into new organisms - such as the malaria parasite Plasmodium Yoelii Yoelii (a model rodent malaria important for understanding the function of human malaria) - to analyze and send to the grid.

The following table describes the data that has recently been or is being processed by the WCG:

Code Experiment Project/Organism Description Status
oa 1169 Microbiome Novel Gastro-Intestinal proteins from the Human Microbiome Project Finished
ob 1169 Microbiome Novel Gastro-Intestinal proteins from the Human Microbiome Project Finished
oc 1169 Microbiome Novel Gastro-Intestinal proteins from the Human Microbiome Project Working...
od 1169 Microbiome Novel Gastro-Intestinal proteins from the Human Microbiome Project Working...
... 1169 Microbiome Novel Gastro-Intestinal proteins from the Human Microbiome Project Working...
og 1169 Microbiome Novel Gastro-Intestinal proteins from the Human Microbiome Project Working...
oh 1169 Microbiome Novel Gastro-Intestinal proteins from the Human Microbiome Project Submitted
oi 1169 Microbiome Novel Gastro-Intestinal proteins from the Human Microbiome Project Submitted
oj 1169 Microbiome Novel Gastro-Intestinal proteins from the Human Microbiome Project Submitted
ok 1169 Microbiome Novel Gastro-Intestinal proteins from the Human Microbiome Project Submitted

Thanks!

--

Duncan Penfold-Brown, Bonneau Lab