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![Overview Technology Software Collabs Outreach Plans
NRNB statistics ‘at-a-glance’
Year 3 of 5 funded years, $700,000 per year direct + $175,000 supplement
4 technology projects with matched driving biology
20 NRNB-supported publications since start of funding
Cytoscape used in ~250 pubs / year and has supported ~1400 NIH grants
96 collaborations with NIH-funded investigators (60 new this year)
27 training events over 7 countries, 32 academic courses by NRNB staff
16 Google Summer of Code Students = $80,000 invested by Google
Representative Publications:
Dutkowski et al. A gene ontology inferred from molecular networks. Nature Biotech. (2013) [cover]
Rügheimer et al. Applications of Intelligent Data Analysis for the Discovery of Gene Regulatory
Networks. Computational Intelligence in Intelligent Data Analysis (2013)
R Saito et al. A travel guide to Cytoscape plugins. Nature Methods (2012)
Cerami et al. The cBio Cancer Genomics Portal. Cancer Discovery (2012)
Morris, S. et al. ClusterMaker: multi-algorithm clustering for Cytoscape. BMC Bioinformatics (2011)
Ideker, T. et al. Boosting signal-to-noise in complex biology: prior knowledge is power. Cell (2011)
Dutkowski et al. Protein networks as logic functions in development and cancer. PLoS Comp Bio (2011).
Fowler et al. Correlated genotypes in friendship networks. PNAS (2011)
Bandyopadhyay and Ideker. Integrated Systems Biology [Poster], Nature Genetics (2010)](https://image.slidesharecdn.com/nrnbmain12dec2012-121217192848-phpapp01/85/NRNB-EAC-Meeting-2012-5-320.jpg)
![Overview Technology Software Collabs Outreach Plans
TRD A: Network Biomarkers (Ideker); DBP 2 (Kipps)
Publication: Chuang et al. Blood (2012) [cover article]](https://image.slidesharecdn.com/nrnbmain12dec2012-121217192848-phpapp01/85/NRNB-EAC-Meeting-2012-12-320.jpg)
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NRNB EAC Meeting 2012
- 1. National Resource for Network Biology External Advisory Council (EAC) Meeting Wednesday December 12, 2012
- 2. Overview Technology SoftwareCollabs Outreach Plans NRNB Overview • An NIGMS Biomedical Technology Resource Center focused on Network Biology • Research and develop new bioinformatic technologies to enable the use of biological networks (molecular, genetic, and social) among NIH-funded investigators • Collaborate directly with biological and clinical users to push the envelope of network analysis capabilities • Distribute open-source network technologies to the greater scientific community • Stimulate a portfolio of educational and outreach opportunities surrounding network biology
- 3. Overview Technology SoftwareCollabs Outreach Plans NRNB Investigators Trey Ideker, PhD Principal Investigator, NRNB Gary Bader, PhD Departments of Medicine and Bioengineering Assistant Professor, Terrence Donnelly Centre University of California, San Diego for Cellular & Biomolecular Research Dr. Ideker uses genome-scale measurements to University of Toronto construct network models of DNA damage Dr. Bader works on biological network analysis response and cancer. He was the 2009 recipient and pathway information resources. of the Overton Prize from the International Society for Computational Biology. James Fowler, PhD Alex Pico, PhD Associate Professor, CalIT2 Center for Wireless & Executive Director, NRNB Population Health Systems and Political Science Gladstone Institute of Cardiovascular Disease University of California, San Diego Staff Research Scientist Dr. Fowler’s research concerns social networks, University of California, San Francisco behavioral economics, evolutionary game theory, Dr. Pico develops software tools and resources and genopolitics (the study of the genetic basis of that help analyze, visualize and explore political behavior). His research on social networks biomedical data in the context of these networks has been featured in Time’s Year in Medicine. Chris Sander, PhD Chair, Computational Biology Center, Benno Schwikowski, PhD Tri-Institutional Professor Chef du Laboratoire/Group Leader Memorial Sloan-Kettering Cancer Center Pasteur Institute Dr. Sander’s research focuses on Computational Dr. Schwikowski’s expertise lies in and Systems Biology of molecules, pathways, and combinatorial algorithms for Computational processes. and Systems Biology.
- 4. The National Resourcefor Network Biology: Integrating genomes & networks to understand health & disease NIH NCRR / NIGMS P41 GM103504 Draft Network Assembly Patient genotype Genome sequencing Phenotype Disease diagnosis Response to therapy/drug Side effects Developmental outcome 1) How to assemble and visualize Rate of aging, etc. Gene expression & network models of the cell? other large scale molecular state measurements 2) How to use networks in healthcare?
- 5. Overview Technology SoftwareCollabs Outreach Plans NRNB statistics ‘at-a-glance’ Year 3 of 5 funded years, $700,000 per year direct + $175,000 supplement 4 technology projects with matched driving biology 20 NRNB-supported publications since start of funding Cytoscape used in ~250 pubs / year and has supported ~1400 NIH grants 96 collaborations with NIH-funded investigators (60 new this year) 27 training events over 7 countries, 32 academic courses by NRNB staff 16 Google Summer of Code Students = $80,000 invested by Google Representative Publications: Dutkowski et al. A gene ontology inferred from molecular networks. Nature Biotech. (2013) [cover] Rügheimer et al. Applications of Intelligent Data Analysis for the Discovery of Gene Regulatory Networks. Computational Intelligence in Intelligent Data Analysis (2013) R Saito et al. A travel guide to Cytoscape plugins. Nature Methods (2012) Cerami et al. The cBio Cancer Genomics Portal. Cancer Discovery (2012) Morris, S. et al. ClusterMaker: multi-algorithm clustering for Cytoscape. BMC Bioinformatics (2011) Ideker, T. et al. Boosting signal-to-noise in complex biology: prior knowledge is power. Cell (2011) Dutkowski et al. Protein networks as logic functions in development and cancer. PLoS Comp Bio (2011). Fowler et al. Correlated genotypes in friendship networks. PNAS (2011) Bandyopadhyay and Ideker. Integrated Systems Biology [Poster], Nature Genetics (2010)
- 6. Overview Technology SoftwareCollabs Outreach Plans Canadian Institutes of Health Research, 23 NICHD, 22 Others, 127 NIDA, 25 Wellcome Trust, 29 NINDS, 39 NIGMS, 354 NIMH, 47 NLM, 54 NHGRI, 58 NIEHS, 62 NCI, 205 NIDDK, 88 NHLBI, 88 NCRR, 110 NIAID, 103 Use of Cytoscape by grantees. We have identified >1,400 grants acknowledged in publications citing a Cytoscape paper (Shannon P et al. 2003; Cline MS et al. 2007; Smoot ME et al. 2011). One pie slice represents the number of grants from a particular agency. NIH institutes are represented by standard abbreviations.
- 7. Overview Technology SoftwareCollabs Outreach Plans NRNB Funding Allocation 1000 Supp-Crowdsourcing 900 Collaboration 800 Outreach Admin-Pico 700 Admin-Ideker 600 Admin-Asst. $1000s 500 Core Comp/Software TRD-A-Ideker 400 TRD-A-Sander 300 TRD-B-Fowler 200 TRD-C-Pico TRD-C-Bader 100 TRD-D-Schwikowski 0 Co-I Salaries Year 1 Year 2
- 8. Overview Technology SoftwareCollabs Outreach Plans Response to previous EAC critiques • Clearly articulate the link between funding and progress See previous chart; all described work is directly funded by NRNB • Focus not only on network visualization but on network-based analysis and decision making Exciting progress has been made for using networks as diagnostic biomarkers under TRD A • Encourage increased citation of Cytoscape Refactored Cytoscape.org to encourage citation; perform systematic literature tracking • Better track Cytoscape plugins and leverage developers Developed new Appstore (apps.cytoscape.org) • Track use of Cytoscape in the classroom Identified 32 courses using Cytoscape in 2011 - 2012
- 9. Overview Technology SoftwareCollabs Outreach Plans Agenda • Progress on Technology Research & Dev. • Release of Cytoscape 3.0 • Review of Collaboration and Service Projects • Progress on Training and Outreach • Plans for NRNB moving forward • Generate discussion and seek advice on all aspects
- 10. Overview Technology SoftwareCollabs Outreach Plans Pico (UCSF)
- 11. Overview Technology SoftwareCollabs Outreach Plans Networks (in various states of curation) Circuits Coupled w/ Decision Tree Logic (or somatic mutation) Patient Expression TRD A: Protein networks as biomarkers of disease Ideker group Janusz Dutkowski et al PLoS Comp Bio 2011
- 12. Overview Technology SoftwareCollabs Outreach Plans TRD A: Network Biomarkers (Ideker); DBP 2 (Kipps) Publication: Chuang et al. Blood (2012) [cover article]
- 13. Overview Technology SoftwareCollabs Outreach Plans TRD A: cBio Cancer Genomics Portal (Chris Sander / MSKCC) http://www.cbioportal.org • Make Cancer Genomics data available to a broad audience: – “Wet lab” biologists involved in functional studies. – Computational biologists • Allow quick access to small data slices (few genes, subset of samples) • Facilitate explorative data analysis / hypothesis generation and testing Cerami et al. 2012, Cancer Discovery
- 14. Overview Technology SoftwareCollabs Outreach Plans Cerami et al 2010, Nucl Acids Res
- 15. Overview Technology SoftwareCollabs Outreach Plans Features for the network view Targeted-drugs Suggesting new targeted-drugs Direct targets (Released) indirect targets (work in progress) Targeted-drug Pathway data data Tumor data Infer and suggest novel, drug-based therapy options Sources: DrugBank, KEGG Drugs, Cancer.gov e.g. AKT inhibitor for PTEN deletion
- 16. Overview Technology SoftwareCollabs Outreach Plans TRD B: Using Cytoscape for Social Network Research Social network of the Hadza hunter-gatherers of Tanzania. This analysis in Cytoscape reproduces the results published earlier this year in Nature by Fowler et al., which show a strong social network-dependence on the donation of public goods across and within groups. The histogram plot is based on the correlation values calculated by CyNetworkSignificance on the original and randomized networks.
- 17. Overview Technology SoftwareCollabs Outreach Plans TRD C: Network Visualization and Representation (Pico / Bader) Visualizing Complex Networks as Ontology-Partitioned Mosaics Mosaic control panel, context menu and tiled result windows. The control panel shows both the color mapping legend and subnetwork display. Context menus for listed subnetworks allow the user to partition deeper within a given ontology branch.
- 18. Overview Technology SoftwareCollabs Outreach Plans • Annotation • Gene set analysis • Edge analysis • Module analysis
- 19. Overview Technology SoftwareCollabs Outreach Plans
- 20. Overview Technology SoftwareCollabs Outreach Plans TRD C: Network visualization and representation (Ideker) Introducing NeXO A Network eXtracted Ontology Janusz Dutkowski et al. Nature Biotechnology (2013)
- 21. Overview Technology SoftwareCollabs Outreach Plans Assembly and alignment of a network-extracted gene ontology
- 22. Overview Technology SoftwareCollabs Outreach Plans
- 23. Overview Technology SoftwareCollabs Outreach Plans
- 24. Overview Technology SoftwareCollabs Outreach Plans TRD D: Inference of Transcriptional Networks (Schwikowski group) • Create „fill-in-the-algorithm‟ infrastructure for inference of gene regulatory networks • Make methods accessible to biologists within the Cytoscape framework Approach: Create a software infrastructure (CYNI) for network inference algorithms
- 25. Overview Technology SoftwareCollabs Outreach Plans Since the last EAC meeting – Summary -C design prototype -Hired engineer Oriol Guitart-Pla (02/15/12) -Working CYNI App -Documented API -User and CYNI App writer documentation -Additional CYNI functionality: Discretization and Imputation -Implemented and documented downloadable “Hello World examples” -CYNI App presented at two French network biology meetings -CYNI App and Comprehensive documentation publicly available
- 26. Overview Technology SoftwareCollabs Outreach Plans
- 27. Overview Technology SoftwareCollabs Outreach Plans TRD Outreach Ideas
- 28. Overview Technology SoftwareCollabs Outreach Plans Cytoscape 3.0 Progress (Core NRNB Software) Major update of technology behind Cytoscape Creates a fully modular architecture and API Cytoscape 2.x would not support the features needed for the current vision of network analysis, e.g. scripting, multiple and 3D renderers, crowd-sourcing, interoperability with web and other tools
- 29. Overview Technology SoftwareCollabs Outreach Plans - Cytoscape 2.x: Maintenance Releases - 2.8.2: Bug fixes and Improved memory allocation - 2.8.3: Bug fixes and better trackpad support for Mac platforms - Cytoscape 3 - 3.0.0 M5: June 2012: For developers - 3.0.0-Beta1: 10/9/2012: First Release for Users - 3.0.0 Final: This Week
- 30. UBE2L3 RRM1 EDIL3 NFKB1 CTBP1 UBE2N POLR2A NME1 OTUB1 JAK1 Overview Technology Software Collabs Outreach Plans PARK2 KPNA1 DNMT1 LAT NF1 XRCC6 VCP EXO1 DNAH8 ENSG00000137337 H2AFX GPR3 SMAD4 HSD17B1P1 FANCD2 BLM STAT1 UBE2D3 WNT2B WWP2 FANCG CDC25C ECHDC1 ID4 ACACA PSAP PARP2 CHGB RCHY1 BRCC3 FBXL7 UIMC1 HERC2 ORC2L C17orf70 C11orf30 TOX3 CASP3 BUB1 9606.ENSP00000358154 XRCC3 ELK4 BIRC5 RNASEL MAP2K1 GSTP1 RNF2 MED17 TRRAP RARB CCNA2 CREBBP EP400 MSH2 NEK2 UBA1 ECT2 PGR GTF2F1 NEK10 YRDC GMNN ORC3L CDK13 DNAJA3 FBXW4 PLK3 HRAS ANTXR1 CDK1 FAM175A JUN FGF11 CDK8 SMARCB1 KRT14 HSPA8 FANCB FBXL3 GATA3 New Features for 3 DDB1 TSPAN17 ARIH1 CDC25A CDC45 PAX6 ELAC2 APLP2 CDKN1A EIF4G1 TOP3A PEG3 PTEN CHEK2 KPNA3 PPP1CA 1 TUBB2A POU2F1 HIC1 CHGA CTCFL PML FLI1 MAP3K4 NUP153 DCAF11 EZH2 RNF31 PIK3CA 2 ERCC2 EGFR SMARCE1 RPA1 GTF2E1 AKAP10 NUSAP1 SMARCC2 FANCA MED21 RAD9A CDKN1B HMMR WRN MLH1 MRE11A ETS1 AP2B1 ESR1 TRIM28 UBE2I SMC1A XRCC5 RBL1 TSPAN9 NMI RNF144B SHFM1 ERCC1 RNF8 HSD17B1 SUGT1 •Edge Bundling WT1 UBC ELK1 RBMXL2 UBB AURKA JUND CNR1 CDK4 MELK PPP1R3A •Welcome Screen SUMO2 ERCC4 BRCA1 LMO7 FBXO4 MDM2 PLK1 NBR1 •New Data Import Clients PMS1 IGF1R TOPBP1 TUBA4A UBA52 FBXO11 TAF2G •Network Annotations PPT1 CSTF1 SMARCA4 RNF168 JUNB TERF2 PPM1D DHFR •Network Collections BATF FBXL5 PALB2 CDK16 FBXO25 SMARCC1 SMARCD2 NCOA3 FAM175B BRCA1 •Enhanced Search MED24 STK11 MED13 PIAS1 WHSC2 CREB1 SMAD3 E2F4 RBBP7 CHD8 ERBB2 BRE HDAC2 WWP1 TP53 LMO4 •Cleaner API MAD2L1 FANCC KIAA1182 EP300 RAD17 BRAP CDK2 HYRC FANCE NUFIP1 PIAS4 DCUN1D1 HIST1H4A PMS2 RNF53 BARD1 •Experimental Headless Mode BRCC1 POLL RBBP8 FANCL CLSPN FGFR2 RFC1 BRCA1 CHTF18 AT2A NBR2 MYC FANCF MAP4K4 SMAD1 TFDP2 GTF2H4 FBXO24 MAP3K3 DCLRE1C DDB2 BRIP1 RAD54B RBL2 RBBP4 BAP1 RNF20 RAD51 DPPA3 AR MPP3 CHEK1 NFYA FBXO9 BUB1B ATF1 RNF11 ZCCHC8 C5orf4 PSMC3IP RPL31 TRAF7 RNF53 PRC1 RELA SCG2 NR1H2 SMURF2 MCM4 SUMO1 UBE3A TADA3 CCNB1 TUBGCP4 RND2 IFI27 INSC RAD51L3 USF2 RAD51C HOXA5 Brca1 TP53BP1 MKI67 COBRA1 TUBG1 FANCI LIG3 SPO11 CDH1 RAD50 TSC1 C19orf40 FBXO21 PCNA CDKN2A FHIT MNAT1 ZNF350 MED23 STAT3 KIF11 CYP17A1 SP1 C19orf62 ERCC3 GADD45A H2AFY DMC1 FBXO7 RASSF1 CSTF2 SRC SIRT1 RFC2 KPNA6 FHL2 ARNT ATRIP DLK1 RAD52 PARP1 EREG XRCC2 ASPM DPH1 BMI1 DHX9 ENSG00000204435 IFI16 AKT1 XPA POU4F1 WDR48 RPA2 CDKL4 MZT1 MSH6 CTCF 30 TIPARP HSD17B2 PIK3R1 GLI1 XRCC4 CCNE1 OPCML
- 31. Overview Technology SoftwareCollabs Outreach Plans Cytoscape 3.0 Advantages: Feature Beneficiary Welcome screen New users (for solicitousness), existing users (for convenience) Import network Experienced users (for ease of use) Edge bend visual property Paper and presentation writers Edge bundling Users of high degree networks Network annotations Users of hierarchical networks Enhanced search Users of highly populated networks Show All in Table Browser Users with highly annotated networks Multiple network management All users Disadvantages: • Unproven stability (i.e., likely numerous bugs) • Slow startup (4 times longer than v2.8) • Fewer plugins (though the missing plugins are the less popular ones) • Larger memory footprint leaves less room (especially on WinXP) for networks 31
- 32. Overview Technology SoftwareCollabs Outreach Plans TRD Outreach Ideas 32
- 33. Number of Members Messages per Month 20,000 40,000 60,000 80,000 0 0 1000 2000 3000 0 50 100 150 200 250 2004-07 2006 01 2004-10 2006 06 2005-01 2006 11 2007 04 2005-04 2007 09 2005-07 2008 02 2005-10 2008 07 2006-01 2008 12 2006-04 A. Website Visits 2009 05 2006-07 2009 10 Total Membership C. Mailing List Traffic 2006-10 2010 03 Discuss Membership Helpdesk Membership 2007-01 2010 08 2007-04 2011 01 D. Mailing List Membership 2007-07 2011 06 2011 11 2007-10 2012 04 2008-01 2012 09 2008-04 2008-07 0 1000 2000 3000 4000 5000 6000 7000 2008-10 2009-01 2004 07 2009-04 2005 01 2009-07 2005 07 2009-10 2006 01 2010-01 2006 07 2010-04 2007 01 2010-07 2007 07 2010-10 2008 01 2011-01 2008 07 2011-04 2009 01 Discuss 2011-07 2009 07 2010 07 B. Number of Downloads 2011-10 2011 01 2012-01 2011 07 2012-04 2012 01 Helpdesk 2012-07 2012 07 2012-10
- 34. Overview Technology SoftwareCollabs Outreach Plans NOW, on to Collaborations Count and scope Highlights Impact
- 35. Overview Technology SoftwareCollabs Outreach Plans COLLABORATIONS • Total: 97 • 60 new collaborations in Year-2 Rejected, 6% Rejected 1 Type of Collaboration External, Ongoing Ongoing, 7 47% 47% 7 53% UCSD, 8 Completed Ended, 7 Consulting 47% only, 3 20% Research collaboration ,7 47% External/Internal Cytoscape Collaboration Requests support, 5 33% *Percentages estimated from UCSD numbers
- 36. Overview Technology SoftwareCollabs Outreach Plans SCOPE of COLLABORATIONS • Applications of Network Tools to Biomedical Research • Frontal Temporal Dementia, Alzheimer’s disease, Diabetes, Anorexia nervosa, Glaucoma, Heart disease, Leukemia, Brain tumors, Autism, Prostate cancer, Breast cancer, Endometrial cancer, Colorectal cancer, Lung cancer, and Malaria. • Inflammation, stem cell differentiation, B-cell differentiation, ciliogenesis, cell-cell communication, oxidative stress response, DNA repair, cancer stem cells, and wound healing. • Interactome, proteomics and metabolomics research. • Development of Cytoscape Plugins/Apps • Connect to public databases • New types of data visualizations • Ontology analysis, graph analysis, partitioning, quantitative modeling. • New data types such as next-gen sequencing data and variant data. • Interoperability with 3D molecular visualization tools, and integrated workbenches. • Development and Application of Other NRNB Tools and Resources • Cytoscape Web in cBio. • Curation of biofuel pathways at WikiPathways • Network analysis functionality to Broad’s IGV (Integrative Genomics Viewer) • Promoting the use of BaSysBio (Bacillus Systems Biology).
- 37. Overview Technology SoftwareCollabs Outreach Plans Actual Request #3(1) Dr. Joseph Gleeson’s lab at UCSD Elucidating miRNA network underlying Ciliome miRNAs Ciliogenesis miRNA faciliating miRNAs transfection (26) Prediction of target Control (25) mRNAs, assessment of enriched GOs In vitro ciliogenesis model: htRPE cell (Serum Ciliogenesis starvetion induces inhibitory miRNAs ciliogenesis in hRPE cells) (55)
- 38. Overview Technology SoftwareCollabs Outreach Plans Yates Laboratory TSRI Jeffrey Savas, PhD Alzheimer's disease Wild type • For protein measurement, N14 is used for Pre 3 month Pre 3 month subject mouse and N15 is used for reference mouse. Log N14 / •Hippocampus •Hippocampus log N15 denotes relative •Cortex •Cortex abundance of corresponding •Cerebellum (Ctrl) •Cerebellum (Ctrl) protein. • Uses PDAPP as mouse model, N5 as second mouse • Dealing with ~18,000 Post 12 month Post 12 month proteins • ANOVA P-values and log2 fold changes are major values •Hippocampus •Hippocampus used for the analyses (more •Cortex •Cortex than two-fold changes and p- •Cerebellum (Ctrl) •Cerebellum (Ctrl) value 0.05 or less) First step is to find proteins whose abundances are altered in hippocampus or cortex, but no alteration in cerebellum. Find candidate proteins which show Map altered proteins onto protein- alteration in protein abundance at protein interaction network statistically significant level (Cytoscape)
- 39. Overview Technology SoftwareCollabs Outreach Plans GSOC’12 Project Collaboration • Mondrian • IGV (Network view) – Broad Institute (work in progress) – Cytoscape 3 application that facilitates acquiring data from cBio Genomics Portal. • Network visualization (cBio Genomics Portal) • Bilkent University, Turkey (iViz Research Group) http://bit.ly/cbioportal
- 40. Overview Technology SoftwareCollabs Outreach Plans
- 41. Overview Technology SoftwareCollabs Outreach Plans IMPACT
- 42. Overview Technology SoftwareCollabs Outreach Plans COLLABORATIONS • 16 GSoC and 5 NRNB Academy students GSoC
- 43. Overview Technology SoftwareCollabs Outreach Plans Outreach • Significant traffic through nrnb.org: a real resource • New content and new development since last EAC Just to make it clear… R01s would not cover this work
- 44. Overview Technology SoftwareCollabs Outreach Plans Cytoscape Workshops 2012 http://nrnb.org/cyretreat/
- 45. Overview Technology SoftwareCollabs Outreach Plans Cytoscape Europe 2013 Date June 5-7, 2013, Institut Pasteur, Paris Audience • New and existing users •New and existing plug-in developers •Researchers interested in network biology Other plans •Present CYNI at other meetings (ICML, ICSB, ...) •Expand CYNI functionality/documentation as needed by new CYNI Apps
- 46. Overview Technology SoftwareCollabs Outreach Plans Ideas and Discussion Topics • Vision for the Technology Research and Development • Additional ways to link social network research (TRD B) with other TRDs • How do we most effectively disseminate resources we have worked so hard to put together: • Better integration with NIH sites/media • Publish many papers: NRNB position paper; Nature protocols; 3.0 paper; App store paper • How do we make sure that NRNB scientists are getting career acknowledgement for non-research activities • Publication tracking issues: • APRSIS is broken (only pulls up 3 NRNB citations). • We need to do much better (10/20 supported papers ref. NRNB). • When is next EAC?
- 47. Overview Technology SoftwareCollabs Outreach Plans Let’s Discuss
- 48. Overview Technology SoftwareCollabs Outreach Plans Additional ideas and topics: • Infovis work on • Multi-dimensional attribute visualization • Interactive alternative views e.g. lenses • E.g. tag cloud lenses at http://www.birdvis.org/ (Juliana Freire) • Intuitive user interfaces for defining interactive filters • Training: Development of interactive workflows • Continue GSoC and NetBio SIG • What else could help to position Cytoscape as a network inference platform of choice in the future? • How can we deal technically with the fact that much academic work ends with a paper and MATLAB code? • What are the best ways for making computationally costly approaches accessible in CYNI? • How can we expand from showing an inferred network to a distribution over networks?
Editor's Notes
- #16 Drug sources – suggest drugs
- #21 Ultimately, the cell is not a flat list of subnetworks or gene clusters, it is a multi-scale hierarchical structure. This structure is well described by the Gene Ontology, the essential gold standard reference of gene function nearly everyone in the field uses. The Gene Ontology is manually-curated by experts which has not scaled well.
- #31 Welcome screen: easy access to data for users
- #32 From a user perspective, the benefits of v3.0 include…And the current disadvantages we have yet to overcome…
- #33 Rintaro’s Nature Methods paper is the first of its kind survey of Cytoscape plugins. Defines transition point to 3.0 and App Store.
- #40 Specific collaboration projects from Sander group
- #41 The NRNB NetworkPeople = blue circlesProjects = gold diamondsPublications = green trianglesNRNB funded = red borderThere are 315 nodes and 404 connections in the network. NRNB funds 41 (13%) of these nodes, which make 217 (54%) of the connections.
- #42 If you remove NRNB from this network… chaos…and wasted potential
- #43 A prominent feature of our collaboration network is GSoC: this summer we mentored 16 GSoC students (largest class yet). Leveraging $80,000 from Google!NRNB.org traffic increases 7-fold during GSoC application week. Averaged over the entire year, it is 4x more popular than any other page on our site.
- #44 The next most popular page is our Training Page, which lists upcoming Training events, Courses and TutorialsNext is the annual NetBio SIG meeting we organize in conjunction with ISMB each year. We just got accepted by ISMB to host for a 3rd year in a row. We are getting great speakers and impressive attendance for this meeting.Also high on the list is our Tools Gallery, which now includes screenshots and citation info. Over the last year, we added Cytoscape Web, WikiPathways and cBio Cancer Portal to the list of NRNB-supported tools.5,000 pageviews/week (cytoscape.org: 15,000 pv/wk)New paradigm for finding functionality in CytoscapeTagged navigation; user ranking and reviewsOne-click installAssisted app submission, including support for apps that export their own APIs for other apps to develop off of!First Cytoscape App Competition – helped get new apps in before 3.0 release – Winner will be announced on Friday during the Cytoscape App Expo