{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2007/10/08/taverna-workshop-day-1-update.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/58bs7-cpq93", "url": "https://chem-bla-ics.linkedchemistry.info/2007/10/08/taverna-workshop-day-1-update.html", "title": "Taverna Workshop, Day 1 Update", "content_html": "

The second part of the morning session featured a presentation by Sirisha Gollapudi which spoke about mining\nbiological graphs, such as protein-protein interaction networks and metabolic pathways. Patterns detection\nfor nodes with only one edge, and cycles etc, using Taverna. An example data she worked on is the Palsson human\nmetabolism (doi:10.1073/pnas.0610772104); she mentioned that this\nmetabolite data set contains cocaine :) Neil Chue Hong finished with\nan introduction on the OMII-UK which is co-host of this meeting.

\n\n

After lunch Mark Wilkinson introduced BioMoby, which we actually use in Wageningen already.\nI have tried to use jMoby to set up services\nbased on the CDK, but failed sofar. Will talk with Mark on that. Next was my presentation,\nand I spoke about CDK-Taverna, Bioclipse and some\npeculiarities with chemoinformatics workflow, like the importance with intermediate interaction, the need to\nvisualize the data and complex, information rich data. Bioclipse is seeing\nan integration of BioMoby and of Taverna.

\n\n

After the coffee brake Marco Roos spoke about myExperiment and his work on text\nmining. I unfortunately missed this presentation, as I was meeting with people from the EBI who work on the\nMACiE database (see\nthis blog item ).

\n\n

A discussion session afterwards introduced a few more Taverna uses, and encountered technical problems.\nTaverna2 is actually going to be quite interesting, with a data caching system between work processors, and a\npowerful scheme of annotation of processors, which will allow rating, finding local services, etc. More on\nthat tomorrow. Dinner time now :)

\n\n

References

\n
\n
Duarte, N. C., Becker, S. A., Jamshidi, N., Thiele, I., Mo, M. L., Vo, T. D., Srivas, R., & Palsson, B. Ø. (2007). Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proceedings of the National Academy of Sciences, 104(6), 1777–1782. https://doi.org/10.1073/pnas.0610772104 CrossRef Scholia
\n
", "summary": "The second part of the morning session featured a presentation by Sirisha Gollapudi which spoke about mining biological graphs, such as protein-protein interaction networks and metabolic pathways. Patterns detection for nodes with only one edge, and cycles etc, using Taverna. An example data she worked on is the Palsson human metabolism (doi:10.1073/pnas.0610772104); she mentioned that this metabolite data set contains cocaine :) Neil Chue Hong finished with an introduction on the OMII-UK which is co-host of this meeting.", "date_published": "2007-10-08T00:10:00+00:00", "date_modified": "2025-03-30T00:00:00+00:00", "tags": ["taverna","ebi","cdk","bioclipse","myexperiment"], "_references": [ { "url": "https://doi.org/10.1073/pnas.0610772104", "doi": "10.1073/pnas.0610772104" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }