Systems Biology Graphical Notation

Competition

An annual competition is organized to stimulate implementation of SBGN support and the use of the notation. The categories in which to compete are better suited either for developers or for end users. Everyone is allow to compete, and the entries are judged by the community.

Categories

Best SBGN software support (1) - Completeness, exactitude, validation

Submit details of your software, including links to the instructions for installation and use. Provide visual proofs that a) your software supports all or most of SBGN languages, b) your software uses the languages accurately, following not only the glyphs but also the syntax and semantics, c) is able to catch or correct mistakes made by users.

Best SBGN software support (2) - Layout and rendering

Submit visual evidence that your software optimize the layout of complex pathways or network, and render SBGN maps in a user friendly manner, combining usability and aesthetics.

Best SBGN map: Breadth, accuracy, aesthetics

This category is geared toward end-user. Provide a high resolution image of your work in SBGN, regardless of the software used to draw it. It can be an SBGN supporting editor, or just a vectorial drawing program.

Best SBGN outreach: lecture, training, publication, book, website

Advocating SBGN will be crucial for its wide adoption. Please provide details of your outreach activity, whether links, multimedia files, printout etc.

Competition 2011

The submission for entries was opened at the HARMONY meeting in April 2011. You can consult the list of entries. Votes must be filled before Sept 23rd 2011.

Below are all the submissions to the SBGN annual competition 2010, grouped by sections. The winners are:

Best SBGN software support

Software must be evaluated according to multiple criteria such as completeness, exactitude, and validation of SBGN or layout and rendering of the maps.

iPAVS

iPAVS -
Website: http://ipavs.cidms.org
Contact: Pradeep Kumar pradeeps@gist.ac.kr
Document describing the submission
iPAVS

SBGN-ED - WINNER

SBGN-ED WINNER
Website: http://www.sbgn-ed.org/
Contact: Falk Schreiber falk.schreiber@uni-konstanz.de
File containing the submission
SBGN-ED

Best SBGN map: Breadth, accuracy, aesthetics

ER Stress response

ER Stress response -
Contact: Pradeep Kumar pradeeps@gist.ac.kr
Document describing the submission
full size map
ER Stress response

KEGG pathways in SBGN - WINNER

KEGG pathways in SBGN WINNER
Contact: Falk Schreiber falk.schreiber@uni-konstanz.de
Document describing the submission
full size map
KEGG

TGF beta signaling pathway

TGF beta signaling pathway -
Contact: Katja Wegner k.wegner@herts.ac.uk
‎Document describing the submission
full size map
TGF beta signaling

Calcium regulation of synaptic plasticity

Calcium regulation of synaptic plasticity -
Contact: Michele Mattioni mattioni@ebi.ac.uk
Document describing the submission
full size map
Calcium regulation

Best SBGN outreach: lecture, training, publication, book, website

Database: iPAVS - WINNER

Database: iPAVS WINNER
Website: http://ipavs.cidms.org
Contact: Pradeep Kumar pradeeps@gist.ac.kr
Document describing the submission
iPAVS

Database: MetaCrop SBGN Maps

Database: MetaCrop SBGN maps -
Website: http://metacrop.ipk-gatersleben.de
Contact: Falk Schreiber falk.schreiber@uni-konstanz.de
‎Document describing the submission
MetaCrop SBGN map

Competition 2010

The submission for entries was opened on April 22nd 2010 and closed on August 15th 2010. You can consult the list of entries. Entries were evaluated by the community between September 1st 2010 and the end of September 2010, each category being subjected to a vote. Results were disclosed at the 2010 annual forum.

Below are all the submissions to the SBGN annual competition 2010, grouped by sections. The winners are:

Completeness, exactitude, validation: SBGN-ED
Layout and rendering: Tie between Arcadia and VISIBIOweb
Best Map: Plant central metabolism
Outreach: Anatoly Sorokin

Best SBGN software support (1) - Completeness, exactitude, validation

BIOCHAM

BIOCHAM -
Website: http://contraintes.inria.fr/BIOCHAM/
Contact: Dragana Jovanovska prijatelkatadadicka@yahoo.com
Document describing the submission
BIOCHAM

CellDesigner

CellDesigner -
Website: http://www.celldesigner.org/
Contact: Yukiko Matsuoka myukiko@sbi.jp
Document describing the submission
CellDesigner

SBGN-ED - WINNER

SBGN-ED WINNER
Website: http://vanted.ipk-gatersleben.de/addons/sbgn-ed/
Contact: Falk Schreiber falk.schreiber@uni-konstanz.de
Document describing the submission
complete submission
SBGN-ED

Best SBGN software support (2) - Layout and rendering

Arcadia - WINNER

Arcadia WINNER
Website: http://arcadiapathways.sourceforge.net/
Contact: Alice Villeger alice.villeger@manchester.ac.uk
‎Complete submission
Arcadia

VISIBIOweb - WINNER

VISIBIOweb WINNER
Website: http://www.bilkent.edu.tr/~bcbi/pvs.html
Contact: Ugur Dogrusoz ugur@cs.bilkent.edu.tr
Complete submission 1
VISIBIOweb

Best SBGN map: Breadth, accuracy, aesthetics

Plant central metabolism - WINNER

Plant central metabolism WINNER
Contact: Falk Schreiber falk.schreiber@uni-konstanz.de
‎Document describing the submission
full size map
Plant central metabolism

Development of Diabetic Retinopathy

Development of Diabetic Retinopathy -
Contact: Bernard de Bono bdb@ebi.ac.uk
Document describing the submission
full size map
Diabetic Retinopathy

Effect of Uranium

Effect of Uranium -
Contact: Anatoly Sorokin asorokin@inf.ed.ac.uk
Document describing the submission
full size map
Uranium effect

Best SBGN outreach: lecture, training, publication, book, website

Tutorial by Yukiko Matsuoka

Article by Falk Schreiber

Tutorial by Anatoly Sorokin - WINNER

Tutorial by Richard Adams