Dahlquist:BOSC ISMB 2016 Notes: Difference between revisions
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=== Posters === | === Posters === | ||
* O30 - Explicit Modeling of Differential RNA Stability Improves Inference of Transcription Regulation Networks by Konstantine Tchourine, NYU - Center for Genomics and Systems Biology | |||
** when using YEASTRACT data, require 1 direct and 2 direct evidence | |||
** Kemmeran KO dataset | |||
** [http://bmcbiol.biomedcentral.com/articles/10.1186/s12915-015-0222-5 Sameith, K., Amini, S., Koerkamp, M. J. G., van Leenen, D., Brok, M., Brabers, N., ... & Apweiler, E. (2015). A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions. BMC biology, 13(1), 1.] | |||
=== Other notes === | === Other notes === | ||
* [http://www.mygoblet.org/ Goblet: Global Organisation for Bioinformatics Learning, Education & Training] | * [http://www.mygoblet.org/ Goblet: Global Organisation for Bioinformatics Learning, Education & Training] | ||
* Android 6 marshmallow allows you to deny access to apps (like location, etc.) | * Android 6 marshmallow allows you to deny access to apps (like location, etc.) |
Revision as of 13:08, 11 July 2016
BOSC/NetBio SIG Day 1 2016-07-08
- Megan Crow spoke at NetBio Sig on Single-cell gene networks from co-expression
- mentioned review on single cell RNA Seq, Grün, D., & van Oudenaarden, A. (2015). Design and analysis of single-cell sequencing experiments. Cell, 163(4), 799-810.
- bar code RNAs before PCR amplification
- MultiQC: Aggregate results from bioinformatics analyses across many samples into a single report
- BOSC Keynote: Jennifer Gardy who is an Assistant Professor of Population and Public Health at the University of British Columbia and a Senior Scientist at the British Columbia Centre for Disease Control (BCCDC)
- Blog summary of BOSC at GigaScience
- Docker
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
Workshop on Education in Bioinformatics (WEB)
- 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
- Matthew Vaughn: Packaging computational biology tools for broad distribution and ease-of-reuse (need to get slides)
- Panel includes these three plus Annette McGrath of the Australian Bioinformatics Network
Posters
- O30 - Explicit Modeling of Differential RNA Stability Improves Inference of Transcription Regulation Networks by Konstantine Tchourine, NYU - Center for Genomics and Systems Biology
- when using YEASTRACT data, require 1 direct and 2 direct evidence
- Kemmeran KO dataset
- Sameith, K., Amini, S., Koerkamp, M. J. G., van Leenen, D., Brok, M., Brabers, N., ... & Apweiler, E. (2015). A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions. BMC biology, 13(1), 1.
Other notes
- Goblet: Global Organisation for Bioinformatics Learning, Education & Training
- Android 6 marshmallow allows you to deny access to apps (like location, etc.)