Dahlquist:BOSC ISMB 2016 Notes: Difference between revisions
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** [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0106479 Ma, S., Kemmeren, P., Gresham, D., & Statnikov, A. (2014). De-novo learning of genome-scale regulatory networks in S. cerevisiae. Plos one, 9(9), e106479.] | ** [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0106479 Ma, S., Kemmeren, P., Gresham, D., & Statnikov, A. (2014). De-novo learning of genome-scale regulatory networks in S. cerevisiae. Plos one, 9(9), e106479.] | ||
** [http://msb.embopress.org/content/6/1/420.abstract Zheng, J., Benschop, J. J., Shales, M., Kemmeren, P., Greenblatt, J., Cagney, G., ... & Krogan, N. J. (2010). Epistatic relationships reveal the functional organization of yeast transcription factors. Molecular systems biology, 6(1), 420.] | ** [http://msb.embopress.org/content/6/1/420.abstract Zheng, J., Benschop, J. J., Shales, M., Kemmeren, P., Greenblatt, J., Cagney, G., ... & Krogan, N. J. (2010). Epistatic relationships reveal the functional organization of yeast transcription factors. Molecular systems biology, 6(1), 420.] | ||
** [http://rnajournal.cshlp.org/content/20/10/1645.short Neymotin, B., Athanasiadou, R., & Gresham, D. (2014). Determination of in vivo RNA kinetics using RATE-seq. Rna, 20(10), 1645-1652.] | ** [http://rnajournal.cshlp.org/content/20/10/1645.short Neymotin, B., Athanasiadou, R., & Gresham, D. (2014). Determination of in vivo RNA kinetics using RATE-seq. Rna, 20(10), 1645-1652.]--key paper | ||
=== Other notes === | === Other notes === | ||
Revision as of 13:59, 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
Talks
- David Gibbs: Solving the influence maximization problem on biological networks; a case study involving the cell cycle regulatory network in Saccharomyces cerevisiae
- Scott Simpkins: Scalable tools for quantitative analysis from sequencing-based chemical-genetic genetic interaction screens
- BEAN-counter for processing barcode sequencing data from multiplexed experiments. Originally designed for chemical genomics experiments performed in the Myers/Boone Labs, it is applicable to any experiment in which pools of genetically barcoded cells are grown under different conditions, with the resulting barcode DNA isolated from those cells combined into one 2nd-gen sequencing run via the use of indexed PCR primers.
- not open source, must obtain license from http://license.umn.edu/technologies/20170001_bean-counter-quantitative-scoring-of-chemical-genetic-interactions
- map index tag to condition
- parse fastq file
- interaction z score
- batch effect correction (unsupervised or ?)
- visualization
- look out for "variance as a function of gene counts"
- BEAN-counter for processing barcode sequencing data from multiplexed experiments. Originally designed for chemical genomics experiments performed in the Myers/Boone Labs, it is applicable to any experiment in which pools of genetically barcoded cells are grown under different conditions, with the resulting barcode DNA isolated from those cells combined into one 2nd-gen sequencing run via the use of indexed PCR primers.
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.
- Ma, S., Kemmeren, P., Gresham, D., & Statnikov, A. (2014). De-novo learning of genome-scale regulatory networks in S. cerevisiae. Plos one, 9(9), e106479.
- Zheng, J., Benschop, J. J., Shales, M., Kemmeren, P., Greenblatt, J., Cagney, G., ... & Krogan, N. J. (2010). Epistatic relationships reveal the functional organization of yeast transcription factors. Molecular systems biology, 6(1), 420.
- Neymotin, B., Athanasiadou, R., & Gresham, D. (2014). Determination of in vivo RNA kinetics using RATE-seq. Rna, 20(10), 1645-1652.--key paper
Other notes
- Goblet: Global Organisation for Bioinformatics Learning, Education & Training
- Android 6 marshmallow allows you to deny access to apps (like location, etc.)
- CatterPlots!!!!!
- Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., ... & Mortazavi, A. (2016). A survey of best practices for RNA-seq data analysis. Genome biology, 17(1), 1.
