Dahlquist:BOSC ISMB 2016 Notes: Difference between revisions
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** [https://datascience.nih.gov/commons NIH Data Commons] | ** [https://datascience.nih.gov/commons NIH Data Commons] | ||
** Instead of funding individual investigators for computational infrastructure, give them credit to use NIH cloud instead, would include training. | ** Instead of funding individual investigators for computational infrastructure, give them credit to use NIH cloud instead, would include training. | ||
* Nirav Merchant: How to Scale Science and People Using the Cloud (slides available after conference on ISMB app) | |||
** University of Arizona | |||
** "computational thinking had become central to our course work" | |||
** local, in-house computational expert: "victim of their own success (denial of service attacks on their availability)" | |||
** users want (chair), send them to home depot | |||
*** [http://starecat.com/content/wp-content/uploads/happy-25th-birthday-ikea-heres-your-cake-self-assembly.jpg Happy Birthday Ikea, here's your cake.x] | |||
** [http://web.mit.edu/evhippel/www/democ1.htm Democratizing Innovation, Eric Von Hippel] | |||
** need managed cloud: CyVerse Atmosphere, iPlant Collaborative, Jetstream | |||
Revision as of 08:00, 11 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
- 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.]
- Oxford Journal Biology Methods and Protocols
- talked to Jennifer Boyd at the booth and suggested the ability to update published protocols with new versions.
- Books
- Gandrud, C. (2013). Chapman & Hall/CRC The R Series : Reproducible Research with R and R Studio. Bosa Roca, US: CRC Press. Retrieved from http://electra.lmu.edu:2110
- library has e-book, but it looks like it is the first edition instead of second edition, limited to a certain number of pages
- Korpelainen, E., Tuimala, J., & Somervuo, P. (2014). Chapman & Hall/CRC Mathematical and Computational Biology : RNA-seq Data Analysis : A Practical Approach. Boca Raton, US: Chapman and Hall/CRC.
- library has e-book, limited to a certain number of pages.
- Gandrud, C. (2013). Chapman & Hall/CRC The R Series : Reproducible Research with R and R Studio. Bosa Roca, US: CRC Press. Retrieved from http://electra.lmu.edu:2110
ISMB Day 2 2016-07-11
- Phil Bourne: The NIH Commons: A Cloud-based Training Environment
- Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., ... & Bouwman, J. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific data, 3.
- NIH Data Commons
- Instead of funding individual investigators for computational infrastructure, give them credit to use NIH cloud instead, would include training.
- Nirav Merchant: How to Scale Science and People Using the Cloud (slides available after conference on ISMB app)
- University of Arizona
- "computational thinking had become central to our course work"
- local, in-house computational expert: "victim of their own success (denial of service attacks on their availability)"
- users want (chair), send them to home depot
- Democratizing Innovation, Eric Von Hippel
- need managed cloud: CyVerse Atmosphere, iPlant Collaborative, Jetstream
