bioinfo-core.org
ISMB 2014: BioinfoCoreWorkshopWriteUp - BioWiki
http://www.bioinfo-core.org/index.php/ISMB_2014:_BioinfoCoreWorkshopWriteUp
Introduction to the Workshop by Brent Richter. Topic 1: Core on a Budget vs Enterprise. Session 2: Community suggested open discussions. Using pipelines within a core. The annual bioinfo-core workshop ran successfully at the 2014 ISMB conference. We had a good attendance for the meeting despite the workshop clashing exactly with the world cup final and we're very grateful for everyone who chose to come along. Introduction to the Workshop by Brent Richter. Earlier in the conference Brent had already prese...
segmine.ijs.si
SegMine methodology
http://segmine.ijs.si/publications
Here is a list of publications which are related to the SegMine methodology, its components (the SEGS algorithm, the Biomine system, etc.). and applications. Mozetič, I., Lavrač, N., Podpečan, V., Kralj Novak, P., Motaln, H., Petek, M., Gruden, K., Toivonen, H., Kulovesi, K. Semantic Subgroup Discovery and Cross-Context Linking for Microarray Data Analysis, In Bisociative Knowledge Discovery. MR Berthold, Ed.), Springer (LNAI 7250), pp. 379-389, 2012. [ pdf. 13, 119 (2012). [ pdf. Mozetič, I., Lavrač...
proteomicsnews.blogspot.com
News in Proteomics Research: Now I have a protein list...what do I do now!??!!?
http://proteomicsnews.blogspot.com/p/sonow-i-have-protein-listwtfourier-do-i.html
News in Proteomics Research. Now I have a protein list.what do I do now! Gustopheles is also confused! Where's my treat, hooman? Do you have a big 'ol protein list from your awesome proteomics core lab and are a little confused about what to do next? This list can't be comprehensive, but maybe I can point you in the right direction.actually.I'll just tell you what I do! More info can be found below as well. First pass - Hijack some ontology tools. Panther is a great place to start. Registration is free a...
segmine.ijs.si
SegMine methodology
http://segmine.ijs.si/download
Download and install SegMine. SegMine is available under GPL licence (the same as Orange and Orange4WS). It is developed on Linux, and works on Linux, Windows, and Mac (not yet tested on Mac). SegMine is implemented as a collection of widgets for Orange4WS, so it requires a working Orange4WS. Environment. We provide binary installers for Orange4WS, SegMine and ZSI (ZSI is required for Orange4WS). Full Orange installer is also provided. Windows systems (XP, Vista, 7):. Orange installation from source.
bioinformatics.knowledgeblog.org
Downstream functional analysis of an ‘omics experiment using freely available tools | The Bioinformatics Knowledgeblog
http://bioinformatics.knowledgeblog.org/2011/06/20/downstream-functional-analysis-of-an-omics-experiment-using-freely-available-tools
A bioinformatics tutorial resource. On June 20, 2011 by Simon Cockell in Transcriptomics. Downstream functional analysis of an ‘omics experiment using freely available tools. In this tutorial, a number of tools for functional analysis will be introduced. We will focus on the downstream analysis of the gene list produced by the Analysing microarray data in R and BioConductor. Hypergeometric tests for over-representation of functional categories. Draws without replacement, from a finite population,. And cl...
orange4ws.ijs.si
SegMine methodology
http://orange4ws.ijs.si/use_cases
Here is an interview about the SegMine methodology with dr. Helena Motaln. From Department of Genetic Toxicology and Cancer Biology. National Institute of Biology. Ljubljana, Slovenia. She shares her opinion on using SegMine in expert data analysis and comments its abilities. We present an example of analysis performed using SegMine. Two datasets were included: the acute lymphoblastic leukemia (ALL) dataset ( Chiaretti et al., 2004. And Schallmoser et al., 2010. Rule discovery using the SEGS algorithm.
orange4ws.ijs.si
SegMine methodology
http://orange4ws.ijs.si/publications
Here is a list of publications which are related to the SegMine methodology, its components (the SEGS algorithm, the Biomine system, etc.). and applications. Mozetič, I., Lavrač, N., Podpečan, V., Kralj Novak, P., Motaln, H., Petek, M., Gruden, K., Toivonen, H., Kulovesi, K. Semantic Subgroup Discovery and Cross-Context Linking for Microarray Data Analysis, In Bisociative Knowledge Discovery. MR Berthold, Ed.), Springer (LNAI 7250), pp. 379-389, 2012. [ pdf. 13, 119 (2012). [ pdf. Mozetič, I., Lavrač...