pre-release: Open Bioinformatics Foundation meeting announcement

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Subject: 
ANN: Open Bioinformatics Foundation at Room 203 Fri July 11, 9:15p


Open Bioinformatics Foundation
=========================
When: 9:15 AM Friday July 11, 2014
Where: Room 203

None

Topics
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1. A History of Bioinformatics (in the Year 2039)
C. Titus Brown

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/1/a-history-of-bioinformatics-in-the-year-2039 
2. ADAM: Fast, Scalable Genomic Analysis
Frank Austin Nothaft

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/2/adam-fast-scalable-genomic-analysis 
3. Automated RNA-seq Differential Expression Validation
Rory Kirchner

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/3/a-framework-for-benchmarking-rna-seq-pipelines 
4. New Frontiers of Genome Assembly with SPAdes 3.1
Andrey Prjibelski

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/4/new-frontiers-of-genome-assembly-with-spades-31 
5. SigSeeker: An Ensemble for Analysis of Epigenetic Data
Jens Lichtenberg

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/5/sigseeker-an-ensemble-for-analysis-of-epigenetic 
6. Galaxy as an Extensible Job Execution Platform
John Chilton

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/6/galaxy-as-an-extensible-job-execution-platform 
7. Open Bioinformatics Foundation (OBF) update
Hilmar Lapp

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/7/open-bioinformatics-foundation-obf-update 
8. Connecting computational steps for NGS, and beyond.
Laurent Gautier

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/47/connecting-computational-steps-for-ngs-and-beyon 
9. Updates to MISO, the open-source NGS LIMS project
Xingdong Bian

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/36/updates-to-miso-the-open-source-ngs-lims-project 
10. Running Taverna Workflows within IPython Notebook
Alan Williams / Aleksandra Pawlik (TBC)

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/37/running-taverna-workflows-within-ipython-notebook 
11. Reconstruction of ancestral genomes in presence of gene gain and loss
Shuai Jiang

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/38/reconstruction-of-ancestral-genomes-in-presence-o 
12. Firehose in The Cancer Genome Atlas: Rigorous Open Science, At Scale
Michael Noble

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/39/firehose-in-the-cancer-genome-atlas-rigorous-ope 
13. GEPETTO Update: An Open Source Framework for Gene Prioritization
Hoan Nguyen

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/40/gepetto-update-an-open-source-framework-for-gene 
14. NeoPipe: An Open Source Framework for Protein sequence analysis
Hoan Nguyen

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/41/neopipe-an-open-source-framework-for-protein-seq 
15. MyGene.info updates: scalable gene-centric web services with user contributions
Chunlei Wu

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/42/mygeneinfo-updates-scalable-gene-centric-web-se 
16. Aiding the journey from data to publication in the plant sciences
Robert Davey

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/43/aiding-the-journey-from-data-to-publication-in-th 
17. Bio2RDF mobile: an app for biological semantic web databases
Maxime Déraspe

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/44/bio2rdf-mobile-an-app-for-biological-semantic-we 
18. WormGUIDES: an Interactive Informatic Developmental Atlas at Subcellular Resolution
Anthony Santella

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/8/wormguides-an-interactive-informatic-development 
19. BioJS: an Open Source Standard for Biological Visualisation
Manuel Corpas

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/9/biojs-an-open-source-standard-for-biological-vis 
20. Biodalliance: a Fast, Extensible Genome Browser
Thomas Down

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/10/biodalliance-a-fast-extensible-genome-browser 
21. TGAC Browser: Visualisation Solutions for Big Data in the Genomic Era
Anil S. Thanki

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/11/tgac-browser-visualisation-solutions-for-big-dat 
22. Explore, Analyze, and Share Genomic Data Using Integrated Genome Browser
Ann Loraine

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/12/explore-analyze-and-share-genomic-data-using-in 
23. BioMart 0.9 - Introducing Tools for Data Analysis and Visualisation
Luca Pandini

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/13/biomart-09-introducing-tools-for-data-analysis 
24. Biocaml: The OCaml Bioinformatics Library
Ashish Agarwal

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/14/biocaml-the-ocaml-bioinformatics-library 
25. BioRuby and Distributed Development
Pjotr Prins

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/15/bioruby-and-distributed-development 
26. Biopython Project Update
Wibowo Arindrarto

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/16/biopython-project-update 
27. Shared Bioinformatics Database Within Unipro UGENE
Ivan Protsyuk

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/17/shared-bioinformatics-database-within-unipro-ugen 
28. Fostering the Next Generation of Data-driven Open Science with R
Karthik Ram

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/18/fostering-the-next-generation-of-data-driven-open 
29. Tripal: an Open Source Toolkit for Building Genomic and Genetic Data Websites and Databases
Margaret Staton

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/46/tripal-an-open-source-toolkit-for-building-genom-0 
30. PLUTo: Phyloinformatic Literature Unlocking Tools
Ross Mounce

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/20/pluto-phyloinformatic-literature-unlocking-tools 
31. A Publication Model that Aligns with the Key Open Source Software Principles
Michael L. Markie

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/21/a-publication-model-that-aligns-with-the-key-open 
32. Codefest 2014 Report
Brad Chapman

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/22/codefest-2014-report 
33. Biomedical Research as an Open Digital Enterprise
Philip Bourne

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/23/biomedical-research-as-an-open-digital-enterprise 
34. Pathview: an R/Bioconductor Package for Pathway-based Data Integration and Visualization
Weijun Luo

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/24/pathview-an-rbioconductor-package-for-pathway-b 
35. Use of Semantically Annotated Resources in the Mobyle2 Web Framework
Hervé Ménager

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/25/use-of-semantically-annotated-resources-in-the-mo 
36. Towards Ubiquitous OWL Computing: Simplifying Programmatic Authoring of and Querying with OWL Axioms
Hilmar Lapp

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/26/towards-ubiquitous-owl-computing-simplifying-pro 
37. Integrating Taverna Player into Scratchpads
Robert Haines

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/27/integrating-taverna-player-into-scratchpads 
38. Small Tools for Bioinformatics
Pjotr Prins

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/28/small-tools-for-bioinformatics 
39. Tripal: an open source toolkit for building genomic and genetic data websites and databases
Margaret Staton

(Needs description.) 
 recording release: yes license:   

40. Tripal: an open source toolkit for building genomic and genetic data websites and databases
Margaret Staton

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/19/tripal-an-open-source-toolkit-for-building-genom 
41. BioBuilds: A Model for Long Term Sustainability of Open Source Bioinformatics
Chris Mueller

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/45/biobuilds-a-model-for-long-term-sustainability-o 
42. SEEK for Science: A Data Management Platform which Supports Open and Reproducible Science
Carole Goble

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/29/seek-for-science-a-data-management-platform-whic 
43. Arvados: Achieving Computational Reproducibility and Data Provenance in Large-Scale Genomic Analyses
Brett Smith

(Needs description.) 
 recording release: yes license: CC BY  
 Video: http://video.open-bio.org/video/30/arvados-achieving-computational-reproducibility 
44. Enhancing the Galaxy Experience through Community Involvement
Daniel Blankenberg

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/31/enhancing-the-galaxy-experience-through-community 
45. Supporting Dynamic Community Developed Biological Pipelines
Brad Chapman

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/32/supporting-dynamic-community-developed-biological 
46. 'Open' as a Strategy for Durability, Reproducibility and Scalability
Jonathan Rees

(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/33/open-as-a-strategy-for-durability-reproducibilit 
47. Panel : Reproducibility: Rewards and Challenges
Phil Bourne, Titus Brown, Varsha Khodiyar,  Kaitlin Thaney


(Needs description.) 
 recording release: yes license:   
 Video: http://video.open-bio.org/video/34/panel-reproducibility-rewards-and-challenges 


Location
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Room 203


About the group
---------------
chapmanb@50mail.com