Reactome: A Curated Pathway Database

Join the Gramene/Plant Reactome Team at PAG 2014

Posted on January 3rd, 2014, by robinhaw, under Conference and Meeting, Reactome Announcement, Reactome Event
The Gramene/Plant Reactome team will be presenting a workshop at the Plant and Animal Genomes (PAG 2014) Conference! Learn the latest updates to Gramene’s comparative genomics and pathways visualization/mining tools to aid your research of plant models and crops.
Workshops will give a broad overview of Gramene’s database resources and demonstrate many specific topics like how to:
  • Explore plant reference genomes with value-added functional annotation, population data, and phylogenomic comparisons
  • Navigate metabolic and regulatory pathways with the new Plant Reactome
  • Analysis of gene expression datasets on Plant Reactome
  • Visualize your data on Gramene’s genome and pathway browsers
  • Mine mutant genes from our extensive germplasm genotype database
  • Download images, sequences, orthologs, gene-trees, and many other data in a variety of conventional formats
  • Give feedback and get help!
Meet with Gramene staff and developers to explore what Gramene can do for you.
Also please VISIT OUR BOOTH for one-on-one assistance or just to say Hi!
Details:

Reactome@ISMB2013

Posted on September 19th, 2013, by robinhaw, under Conference and Meeting

ISMB2013 is in Berlin this year and Reactome will be there. Robin Haw will be talking at the Network Biology SIG Meeting on Friday, July 19th and presenting a poster at the main ISMB conference (A078).

Reactome Webinar Series

Posted on September 28th, 2012, by robinhaw, under Conference and Meeting, Reactome Meeting

Reactome is hosting a new series of webinars that will introduce the website and our suite of pathway and network visualization and analysis tools. The first two sessions will start in October, and will be repeated every month. Additional webinar topics will be added to the future schedule.

The first session on 8th October will describe Using Reactome Pathway Database. On 15th October, the second session will introduce the Reactome Functional Interaction Network Cytoscape plugin. If you are interesting in participating, please register at Eventbrite.

Feel free to pass this invitation along to colleagues who may benefit from learning about Reactome.

Registrants will receive detailed instructions about accessing the webinar via e-mail the Friday prior to the event. (Anyone registering between Friday and the close of registration will receive the message shortly after the registration is received, within normal business hours.)

Version 42 Released

Posted on September 21st, 2012, by robinhaw, under Conference and Meeting, Reactome Publication, Reactome Release Announcement

Topics with new or revised events include Immune system (STING mediated induction of type 1 IFN and DAP12 Interactions and signaling), Disease (Mucopolysaccharidoses and Signaling by PI3K/AKT in Cancer), Cell Cycle (Golgi Cisternae Pericentriolar Stack Reorganization), Metabolism (Regulation of Cholesterol Biosynthesis by SREBP), Metabolism of proteins (Metabolism of Angiotensinogen to Angiotensins), Membrane Trafficking (GLUT4 Translocation), and Gene expression. S AlvesJL AshworthA ColanziMF CoutinhoL JinJ JosephA KlipLL LanierG LiangF RauscherL ThorpeY WangH Yuzugullu, and J Zhao are our external reviewers. New pathway illustrations for this release include Signal transduction Signaling by Hippo, Signaling by SCF-KIT, and Mitochondrial Protein Import. Reactome is hosting two webinars, Using Reactome Pathway Database and Reactome Functional Interaction Network plugin in October. If you are interesting in participating, please register at Eventbrite. A new paper entitled Reactome – a curated knowledgebase of biological pathways: megakaryocytes and platelets has been published in the Journal of Thrombosis and Haemostasis.


Reactome will be attending COMBINE 2012

Posted on June 29th, 2012, by robinhaw, under Conference and Meeting

The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats, initially in Systems Biology and related fields. The Annual COMBINE forum is a workshop-style event with oral presentations, posters and breakout sessions.  The meeting provides an opportunity for those involved in many related standardization and software efforts in systems biology to meet and discuss their efforts, with the aim of working more closely together to ensure smooth interoperability between systems.

COMBINE 2012 will take place at The Donnelly Centre building at the University of Toronto from Wednesday August 15 to Sunday Aug. 19, 2012, immediately preceding the 13th International Conference on Systems Biology. The COMBINE conference location is a short walk from ICSB events and COMBINE 2012 is an official satellite meeting of ICSB, so you can follow the same travel and accommodation instructions for ICSB and use the same hotel discounts. Registration for COMBINE is $125 (Canadian) to cover costs associated with the meeting, including a workshop dinner and catering.

We hope to see you there!

Psimex: Network and Pathways Bioinformatics for Biologists: 16-18 May 2012 @ EBI

Posted on January 9th, 2012, by robinhaw, under Conference and Meeting, Workshop

Title: Network and Pathways Bioinformatics for Biologists
Date: 16 – 18 May 2012
Venue: EBI, Wellcome Trust Genome Campus, Hinxton

Course Overview

Is it right for me?
This practical course is specifically intended to give life scientists training on how to optimally explore and use protein-protein interaction bioinformatics resources. This course spans from the actual data repositories to resources and tools to explore and analysis the vast amounts of data available. We will also cover data resources related to pathways. Principles of biological network analysis will be introduced and case studies presented. Preference will be given to those actively involved in or commencing protein interaction and/or pathway-related projects.

What will I learn?

· Molecular interactions state of the art
· Making sense of interactions
· Interactions: regulation at the molecular, systems and genome level
· Network based tools for novelty finding
· Pathways informatics: databases and tools
· Ontologies and Standards in Interactions and Pathways

For further information or to register for this course please follow this link: http://www.ebi.ac.uk/training/onsite/120516_intpathpsimex.html

Reactome is participating in GSoC 2011 Mentor Summit

Posted on October 22nd, 2011, by robinhaw, under Community News, Conference and Meeting

Reactome is one of 175 open source projects participating in the Google Summer of Code (GSoC) Mentor Summit on October 22-23 in Mountain View, California. This two-day unconference provides a unique opportunity for developers from projects worldwide the opportunity to meet, network and find common ground in the pursuit of making the GSoC program and open source development even more successful.

Version 3 of the FlyReactome Knowledgebase has been released

Posted on July 23rd, 2010, by robinhaw, under Conference and Meeting

Version 3 of the FlyReactome Knowledgebase has been released and is accessible at http://fly.reactome.org.

FlyReactome (Mark Williams and Michael Ashburner at the Dept. of Genetics, Univ. of Cambridge), developed in collaboration with the Reactome Knowledgebase group (www.reactome.org), covers Drosophila melanogaster signalling processes. The information in FlyReactome is provided by expert biological researchers and edited and maintained by the FlyReactome staff. New material is peer-reviewed and revised as necessary before publication to the web. FlyReactome entries are linked to corresponding ones in FlyBase, UniProt, NCBI (GeneID and RefSeq), Ensembl, BioGPS, CTD, KEGG (Genes and Compound), ChEBI, PubMed and Gene Ontology (GO).

The web interface allows users to view the curated annotations of the following signalling pathways: Wingless, JAK/STAT, Imd, Toll, Hedgehog, Circadian Clock, Hippo/Warts, and Planar Cell Polarity.   The last three are new pathways released in Version 3.

An Editorial Calendar, under the Content menu, containing future and pending (awaiting review) pathways is available. A basic Search Tool is available on the front page while a more powerful Advanced Search option can be accessed from the Tools menu.

Data download including database dumps and protein-protein interaction datasets are available from the download page on the website. FlyReactome data can be exported in SMBL, Protégé, and BioPAX level 2 and level 3 formats. Like everything in FlyReactome, these downloaded and exported materials can be reused. Users can subscribe to Reactome announcement list from the webpage at http://mail.reactome.org/mailman/listinfo/reactome-announce.

FlyReactome is seeking expert help for the review of new modules. The FlyReactome knowledgebase relies on collaborations with research biologists to construct expert consensus views of key signalling pathways, and to integrate these with other processes already in FlyReactome. If you’re interested, please contact us at mgw29@gen.cam.ac.uk.

For questions and comments concerning the Reactome project in general please reply to this message or write to help@reactome.org.

-The FlyReactome project

Reactome@ISMB2010

Posted on July 7th, 2010, by robinhaw, under Conference and Meeting

ISMB2010 is in Boston this year and Robin Haw, Christina Yung, and Lincoln Stein will be attending. Robin will be talking at the 11th BioPathways – SIG Meeting on July 9th and presenting a poster entitled The Reactome Reloaded (E17). Lincoln Stein will be presenting Visualization of biological networks during the Special Session #5 on July 13th from 10:45 a.m. – 12:40 p.m in Room 312. After Lincoln’s session, Robin will be at the EBI Booth (#23) from 1:00 p.m. – 2:00 p.m to talk to ISMB attendees about Reactome.