Reactome

New Reactome Publication

Robin Haw — Tue, 18 Jun 2013 22:55:54 +0000

A new Reactome paper has been published in Methods in Molecular Biology. More publications from the Reactome Team can be found here.

21 New Rice Pathways at Plant Reactome

Robin Haw — Tue, 11 Jun 2013 13:50:22 +0000

The Plant Reactome group has released 21 new rice pathways, focusing on carbohydrate biosynthesis, cofactor biosnythesis, and secondary metabolite biosnythesis.

New Reactome Publication

Robin Haw — Tue, 11 Jun 2013 13:13:25 +0000

A new Reactome paper has been published in Chemistry and Biology.

Reactome Training Online

Robin Haw — Fri, 26 Apr 2013 17:43:36 +0000

If you are new to Reactome or interested in learning more about our pathway vizualisation and analysis tools, you can view these online courses: Quick Tour of Reactome and Reactome: Exploring and Analysing Biological Pathways.

SBGN – A Survey of Pathway Diagrams

Robin Haw — Fri, 26 Apr 2013 17:35:30 +0000

Could you spend a little time to complete a short survey about Biological Pathway diagrams?

For a number of years now a community of like minded Systems Biologists have been developing a graphical notation that aims to systematically and unambiguously draw biological pathways. Our aim has been to permit the exchange of pathway information graphically without the need for supporting text. We call this standard the Systems Biology Graphical Notation (SBGN). You can find out more at http://www.sbgn.org.

We would like to understand how widely SBGN is used and whether the notation meets your needs and so we have developed our survey.

It would be of great assistance to us if you could complete the survey by following the link below. It will only take about 10 minutes of your time.

http://www.surveymonkey.com/s/96ZFGCV

Kind regards,

The SBGN Editorial Board.

Reactome will be taking part in Google Summer of Code 2013

Robin Haw — Mon, 08 Apr 2013 19:08:25 +0000

The Genome Informatics group, organizing the joint efforts of Galaxy, GBrowse, Generic Model Organism Database (GMOD), JBrowse, Reactome, Wormbase, PortEco and SeqWare will be participating in the Google Summer of Code 2013. Here is the complete list of the accepted organizations, chosen by Google to take part in this exciting program. This is a great opportunity for undergraduate students to contribute to the work of these bioinformatics projects, to participate in open source development, and to do work related to their academic pursuits during the summer. Students wishing to apply for Google Summer of Code will have the next two weeks to learn more about the accepted projects before student applications open on Monday, April 22 at 19:00 UTC. More information about the project ideas and the GSoC program is available on the GMOD website. If you have any questions or queries, please feel free to send a post to the Genome Informatics Google Groups.

Version 44 Released

Robin Haw — Thu, 14 Mar 2013 17:00:52 +0000

New to Reactome is Binding and Uptake of Ligands by Scavenger Receptors. Topics with new or revised events include Immune system (Fcgamma receptor (FCGR) dependent phagocytosis), Cell Cycle (Resolution of Sister Chromatid Cohesion, Regulation of PLK1 Activity at G2/M Transition, Nuclear envelope breakdown, and Initiation of Nuclear Envelope Reformation), Extracellular matrix organization (Fibronectin matrix formation and Elastic fibre formation), Metabolism (Ubiquinol biosynthesis and cytosolic-nuclear iron-sulfur cluster biogenesis), Signal Transduction (Signaling by TGF-beta Receptor Complex, Signaling by NOTCH2, and Visual phototransduction), Transmembrane transport of small molecules (Stimuli-sensing channels), and Disease (Diseases associated with visual transduction, and Signaling by NOTCH1 in cancer). New pathway illustrations for this release include Apoptosis Extrinsic pathway and Trafficking and processing of endosomal TLRs. R Lill is our external author. J Avruch, W Blaner, V Fiorito, L He, M Kawamukai, I Mattaj, S Moestrup, J Parkinson, F Rauscher, D Reinhardt, C Rosales, Y Tanno, E Tolosano, EJ Uringa, Y Watanabe, and R Weil are our external reviewers. Plant Reactome, an integrated analysis and visualization platform for plant metabolic and regulatory pathways and networks has been released. Reactome is actively soliciting feedback through a User Survey in order to assess community needs.

Reactome User Survey 2013

Robin Haw — Tue, 26 Feb 2013 20:38:19 +0000

Reactome is committed to providing access to high-quality pathway information and helpful data analysis and visualization tools. With this in mind, we are actively soliciting comments from the research community in order to assess community needs. We are interested to hear about your experiences with Reactome, and would like to know a bit about your background and research interests so that we can continue to improve the Reactome website and tools.

The survey should take about 5 minutes to complete. The information you provide will never be made publicly available or shared with third parties. Participation in the survey is optional, however, five lucky participants who complete the survey will receive a Reactome T-shirt.

Please spread the word to other friends and colleagues who use Reactome. Your feedback is vital in helping Reactome to serve its user community!

You can access the survey at: http://www.surveymonkey.com/s/reactomesurvey2013

Google Summer of Code 2013 Announced

Robin Haw — Mon, 25 Feb 2013 03:53:09 +0000

Google Summer of Code 2013 has been officially announced. The Google Summer of Code is a mentoring scheme in which software developers from across the open source community pass on their knowledge to the next generation of coding enthusiasts. This year, the Genome Informatics Group, organizing the joint efforts of Wormbase, Reactome, SeqWare, GMOD, Galaxy, JBrowse, and Gbrowse will apply to participate in this year’s GSoC program. More information on project ideas and the program will be published at the GMOD website. If you have any questions, project suggestions, or interested in mentoring students, please feel free to send a post to the Genome Informatics Google group or contact robin.haw [at] oicr.on.ca. Student applicants will need to wait a little longer until the list of participating organizations is released in March.

Version 43 Released

Robin Haw — Wed, 19 Dec 2012 14:00:26 +0000

Topics with new or revised events include Immune system (TLR4 cascade, MyD88:Mal cascade on plasma membrane, and MyD88-independent cascade), Cell Cycle (Condensation of prometaphase chromosomes, Mitotic prophase: MASTL facilitates mitotic progression, and Resolution of sister chromatid cohesion), Extracellular matrix organization (Collagen degradation, Elastic fibre formation, and Assembly of collagen fibrils and other multimeric structures), Metabolism (Inositol Phosphate Metabolism, Arachidonic acid metabolism, Mitochondrial Iron-Sulfur Cluster Biogenesis, and Phosphate bond hydrolysis by NUDT proteins), Signal Transduction (Signaling by Activin and Signaling by IGF1R), and Gene expression. New pathway illustrations for this release include Cell Cycle and Apoptosis. R Lill is our external author. A Burgess, YG Chen, KA Fitzgerald, F Granucci, M Holzenberger, R Ito, S Kalamajski, V Malhotra, V Mochida, L Muiznieks, J Napetschnig, S Raleigh, F Rauscher, S Ricard-Blum, TA Rouault, M Rush, T Sorsa, WH Tong, T Wundenberg, I Zanoni, and N Zhang are our external reviewers. Reactome’s SBML export (available here) has been upgraded to Level2 Version4. Our SOAP and RESTful web services, have been moved to a new server. A new series of webinars, which will introduce the Reactome website and our suite of pathway and network visualization and analysis tools, will restart in January 2013. Registration details can be found on EventBrite. A new paper, describing the extension of the Reactome data model and enhancing the web tools to permit the annotation and visualization of protein variants, anti-cancer therapeutics, and other disease processes using Reactome, was published in Cancers.