BioAssist_NL2011-11-22T12:34:33+00:00/groups/192013-05-08T14:51:52+00:00Marco Roos shared BioAID_EnirchBioModelWithProteinsFromTextThis workflow is for demonstration purposes only. Please contact the authors if you wish to try it. We will gladly collaborate with you. Summary This workflow extracts proteins and protein relations from Medline. Extracted protein names (symbols of at least 3 characters) are validated against mouse, rat, and human UniProt symbols, so the results are limited to these species. This workflow follows the following basic steps: it retrieves documents relevant for the query string it discovers proteins in those documents, that are considered relevant to the query string and related to the proteins mentioned in the query (colocation in text mining jargon) it stores the results in a semantic repository To support hypothesis formation, the results are added to a repository containing proto-ontologie …urn:uuid:5638ddc6-e3b3-4655-9200-e00bc751d2c3Marco Roos2010-11-17T19:15:38+00:00Ishtiaq AHMAD shared Warp2D - 2D Time Alignment Workflow2D Time Alignment We describe a new time alignment method that takes advantage of both dimensions of LC-MS data to resolve ambiguities in peak matching while remaining computationally efficient. This approach, Warp2D , combines peak extraction with a two-dimensional correlation function to provide a reliable alignment scoring function that is insensitive to spurious peaks and background noise. One-dimensional alignment methods are often based on the total-ion-current elution profile of the spectrum and are unable to distinguish peaks of different masses. Warp2D - 2D Time Alignment Warp2D is an efficient, fundamentally new approach to correct for non linear retention time shifts between complex proteomics and metabolomics LC-MS data sets. Warp2D operates on peak lists and use the integral of …urn:uuid:51c5a799-fc49-466c-875e-729149701c7aIshtiaq AHMAD2009-11-10T09:36:54+00:00Ishtiaq AHMAD joined the BioAssist_NL groupurn:uuid:ff757465-89dd-470f-8415-3b00c4a426aeIshtiaq AHMAD2009-10-26T23:04:24+00:00Rob Hooft joined the BioAssist_NL groupurn:uuid:3cbcee0d-8c3c-49ad-9106-4c6813cb1452Rob Hooft2009-10-26T23:04:11+00:00Jbot joined the BioAssist_NL groupurn:uuid:e46b6b7a-39be-4f8a-9069-f0eff7c17719Jbot2009-10-26T23:03:58+00:00Barbera van Schaik joined the BioAssist_NL groupurn:uuid:1a4ae731-0406-41b5-920d-ae5865cf9b21Barbera van Schaik2009-10-26T23:03:40+00:00Michaelvanvliet joined the BioAssist_NL groupurn:uuid:045237d2-aa3e-41ce-a0d5-a29ab1b8fad3Michaelvanvliet2009-10-26T23:03:26+00:00Wim spee joined the BioAssist_NL groupurn:uuid:bd13b575-5cec-4655-bf6f-20d1696fbf15Wim spee2009-10-26T10:15:06+00:00Barend shared The general plan and guidelines for BioAssist from October 2009-?This document has been accepted at the NBIC management team meeting of 22 October 2009, and will serve as ageneral guideline to run the BioAssist program of NBIC. It might be a good idea to read the short document before you contact BioAssist for support in the scope of your 'code' or 'content' interests. Barend Monsurn:uuid:84185b2e-7362-4df1-b7c5-51840eb5d793Barend2009-07-30T13:06:37+00:00Barend joined the BioAssist_NL groupurn:uuid:944e3f64-0a8b-4d1d-881a-0744d93c9686Barend2008-11-30T21:07:54+00:00Alexg joined the BioAssist_NL groupurn:uuid:2b78b10c-4254-4c93-b6f6-7affeb27652bAlexg2008-11-29T14:33:31+00:00Angela Luijf joined the BioAssist_NL groupurn:uuid:c7d8f0f6-ced4-4cfb-8a35-42dac26ebc60Angela Luijf