Dahlquist:BOSC ISMB 2016 Notes: Difference between revisions
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** STRING-DB, when comparing data from different protein-protein interaction data, need to calibrate raw quality scores against gold standard (KEGG), see [http://nar.oxfordjournals.org/content/33/suppl_1/D433.full von Mering et al 2005] | ** STRING-DB, when comparing data from different protein-protein interaction data, need to calibrate raw quality scores against gold standard (KEGG), see [http://nar.oxfordjournals.org/content/33/suppl_1/D433.full von Mering et al 2005] | ||
** text-mining snafu, human gene nomenclature committee approved human gene called "SDS" | ** text-mining snafu, human gene nomenclature committee approved human gene called "SDS" | ||
* Talk by Natasa Przulj | |||
** http://www.nature.com/articles/srep04547 [Yaveroğlu, Ö. N., Malod-Dognin, N., Davis, D., Levnajic, Z., Janjic, V., Karapandza, R., ... & Pržulj, N. (2014). Revealing the hidden language of complex networks. Scientific reports, 4.] | |||
** small motifs/legos in networks | |||
** [http://science.sciencemag.org/content/353/6295/123 Nataša Pržulj, Noël Malod-Dognin (2016) Network analytics in the age of big data Science 08 Jul 2016:Vol. 353, Issue 6295, pp. 123-124 DOI: 10.1126/science.aah3449] |
Revision as of 09:07, 10 July 2016
BOSC/NetBio SIG Day 1 2016-07-08
BOSC SIG Day 2 2016-07-09
- MetaR from Fabien Campagne lab
- potentially collaborate on a grant; broader impacts of teaching MetaR to undergrads
- GenePattern Notebooks
- an integrative analytical environment for genomic research; can do RNAseq analysis
- available on Indiana University supercomputer cluster
- ReportMD
- uses R markdown to generate linked HTML reports
ISMB Day 1 2016-07-10
- COSI/SIG SysMod (formerly BioPathways)
- iPath: Interactive Pathways Explorer
- Talk by Lars Juhl Jensen
- STRING-DB, when comparing data from different protein-protein interaction data, need to calibrate raw quality scores against gold standard (KEGG), see von Mering et al 2005
- text-mining snafu, human gene nomenclature committee approved human gene called "SDS"
- Talk by Natasa Przulj
- http://www.nature.com/articles/srep04547 [Yaveroğlu, Ö. N., Malod-Dognin, N., Davis, D., Levnajic, Z., Janjic, V., Karapandza, R., ... & Pržulj, N. (2014). Revealing the hidden language of complex networks. Scientific reports, 4.]
- small motifs/legos in networks
- Nataša Pržulj, Noël Malod-Dognin (2016) Network analytics in the age of big data Science 08 Jul 2016:Vol. 353, Issue 6295, pp. 123-124 DOI: 10.1126/science.aah3449