WikiPathways Summit 2018
To celebrate 10 years of open science, the WikiPathways team is hosting a 3-day summit at Gladstone Institutes in San Francisco featuring seminars and hands-on workshops.
Each day of the event is themed to serve the various communities of users and contributors working with biological pathways. Anyone interested in pathways is welcome to attend. No prior experience with WikiPathways is required.
Day 1—Monday, October 8, 2018
Researcher Community Summit and Workshops
The first day will include presentations on active research incorporating pathway analysis in fields of development, immunology, cancer, toxicology, and metabolomics.
- Alex Pico, Gladstone Institutes—Ten Years of Open Science
- Chris Evelo, Maastricht University, The Netherlands—A Path Across the Ocean
- Shomyseh Sanjabi, Gladstone Institutes—Deciphering the Pathways Leading to HIV Latency in Patient-derived CD4 T Cells
- Nathan Salomonis, Cincinatti Childrens Hospital Medical Center—From Single Cell Analysis to Pathways
- Linda Rieswijk, University of California Berkeley—Using the Key Characteristics of Human Carcinogens in a Data-Driven Approach to Improve Carcinogenicity Prediction and Chemical Prioritization
- Jalal Khalid Siddiqui, Ohio State University—Applications of RaMP: A Comprehensive and Integrated Relational Database of Metabolomics Pathways
- Charlotte Nelson, University of California at San Francisco—Generating Deep Patient Stratification by Propagating Individual Electronic Medical Records Through A Knowledge Network
- Eric Jaehnig, Baylor College of Medicine—LinkedOmics: Analyzing Multi-omics Data within and across 32 Cancer Types
- Workshop 1—Introduction to Pathway Enrichment Analysis and Data Overlays for Non-Programmers
- Workshop 2—Scripting Pathway Analysis and Data Overlays for Programmers
Day 2—Tuesday, October 9, 2018
Biocurator Community Summit and Workshops
The second day will focus on the task of biocuration and include presentations on best practices and current challenges from a variety of pathway resources.
- Denise Slenter, Maastricht University, The Netherlands—Challenges in Curating Biological Databases
- Robin Haw, Ontario Institute for Cancer Research, Canada—Reactome: A Pathway Knowledgebase
- Sushma Naithani, Oregon State University—Involving the Community in Plant Genes and Pathway Curation
- Marvin Martens, Maastricht University, The Netherlands—Introducing a New Type of Pathway to WikiPathways
- Emek Demir, Oregon Health and Science University—Machine Assisted Biocuration: Insights from the DARPA’s Big Mechanism and Communicating with Computers programs
- Laurent-Philippe Albou, University of Southern California & Lawrence Berkeley National Laboratory, Affiliate—Gene Ontology Causal Activity Models: An OWL Representation of Biological Function in the GO
- Egon Willighagen, Maastricht University, The Netherlands—Automated Curation with Internal and External Validation
- Martina Summer-Kutmon, Maastricht University, The Netherlands—Latest Updates in the PathVisio Pathway Editing Tool
- Workshop 1—Introduction Pathway Modeling for Biologist and New Biocurators
- Workshop 2—Survey of Tools and Resources with Developers for Experienced Biocurators
Day 3—Wednesday, October 10, 2018
Developer Community Summit
The last day will drill down into the code and maintenance of public scientific databases, seeking sustainable and collaborative development strategies.
- Martina Summer-Kutmon, Maastricht University, The Netherlands—WikiPathways: Past and Future
- Mark Hershberger, NicheWork, LLC and Victoria Coleman, Wikimedia Foundation—[Panel] Wikimedia:Putting the Wiki into Pathways
- Ben Good, Lawrence Berkeley National Laboratory, Affiliate—Integrating BioPAX Pathways with Gene Ontology Causal Activity Models
- Egon Willighagen, Maastricht University, The Netherlands—Using WikiPathways with Its Resource Description Framework Format
- Zak King, University of California, San Diego—[Demo] Introduction to Escher Pathway Builder
- Robin Haw, Ontario Institute for Cancer Research, Canada—[Demo] Reactome Pathway Editor
- Anders Riutta, Gladstone Institutes—Pathway Figure Optical Character Recognition
- Chris Evelo, Maastricht University, The Netherlands—The Path to a Pathway Community
- Two rounds of unconference-style breakout sessions
This program is intended for open source software developers interested in building tools and resources to enhance pathway representations and usage in biomedical research.
Registration to the summit and workshops are free and includes lectures and presentations. However, please register separately for the workshops on days 1 and 2 using the link above.
WikiPathways is dedicated to providing a harassment-free and inclusive event experience for everyone. Please review our event policy if you plan to pariticpate in any online or in-person event hosted by WikiPathways.
This summit is organized as a collaboration between Alexander Pico’s group at Gladstone and Chris Evelo’s team at Maastricht University in the Netherlands.