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Domain: cytoscape.org

Stories and comments across the archive that link to cytoscape.org.

Comments · 7

  1. Re:Auto-ordering graphs? yed has done this for yea by Anonymous Coward · · Score: 4, Informative · on Kyoto Prize Laureate Unsnarls Electronic Networks

    Another great piece of graphing software: Cytoscape.

  2. R Bioconductor Cytoscape EGAN by bzdyelnik · · Score: 3, Informative · on Open Source Software Meets Do-It-Yourself Biology

    Don't forget R/Bioconductor! Not only is R free/free, but there are thousands of available Bioconductor packages ready for out-of-the-box use. Also consider Cytoscape and or EGAN for graph visualization of established and experimental bio-knowledge. http://www.bioconductor.org/ http://www.cytoscape.org/ http://akt.ucsf.edu/EGAN/ (full disclosure - I work on EGAN)

  3. InforSense by TheTrooper · · Score: 1 · on Visualizing Complex Data Sets?

    Coming from a data mining background, InforSense's platform allows you to not only manipulate your data, perform calculations (and data mining) but then visualize your results in an AJAX environment. You can call open source apps like R and Cytoscape directly from InforSense's workflow building application, so none of your pre-existing work gets discarded.

  4. Cytoscape by adamkennedy · · Score: 4, Informative · on Visualizing Complex Data Sets?

    I had a similar situation to yours recently, except I was trying to detangle a horridly complex product substitution graph for a logistics company.

    I used a bunch of Perl to crunch the raw databases into various abstract graph structures, but instead of graphviz or something created by/for developers, I found that the best software for graph visualisation is the stuff that the genetics and bio people use.

    The standout for me was a program called Cytoscape which can import enormous graph datasets and then gives you literally dozens of different automated layout algorithms to play with (most of which I'd never heard of, but it's easy to just go through them one at a time till something works)

    It's got lots of plugins for talking to genetics databases and such, but if you ignore all that and use Perl/Ruby/whatever for the data production part of the problem, it's a great way to visualise it.

  5. Cytoscape by Jello7 · · Score: 1 · on Mapping/Understanding System Complexity?

    A better tool than GraphViz for this application is Cytoscape - http://cytoscape.org/ It was originally designed for biological applications, but is a general network visualizer with a very simple input format e.g.

    ModelA-Charlie dependsOn ModelQ
    ModelQ requires Java
    etc.

    You can visualize, interact with and edit the resulting network and even do some advanced analyses, such as network clustering which would tell you which families of projects you have.

    It is written in Java and is LGPL.

  6. Cytoscape. by Anonymous Coward · · Score: 1, Informative · on Global DNA Project to Study Human Ancestry

    http://www.cytoscape.org/

    "Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data."

    http://www.geneontology.org/

    "The goal of the Gene Ontology project is to produce a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing. GO provides three structured networks of defined terms to describe gene product attributes. GO is one of the controlled vocabularies of the Open Biomedical Ontologies."

  7. Finally a Slashdot Article about this! by rowanxmas · · Score: 5, Interesting · on Graphing Libraries for Java?
    It just so happens that I have done a lot of work in this area. Specifically in the business of making a good Open Source Java Graph library. For me there were several concerns.
    1. Open Source, Free
    2. Really Cool Looking Display
    3. Easy to add to
    4. Easy to use API
    5. Suited to my work ( Biology )
    At the time we were using yFiles, but it has several problems. Mainly, it is pay-for-it software, and hard to extend (i.e. no Interfaces, Node and Edge are final, not Open Source, so no custom code was possible.) However, yFiles has better layout than anyone else in this field.

    After evaluating many packages (which are listed here) which include the ones you have listed. We decided that our needs were not met and built our own. (First one on the preceding link) The main thing that I needed was a flexable UI, for showing Multi-Dimensional Data, and support for subgraphs, in a way that makes lots of sense in how I work, but I am not sure if it is suitable elsewhere yet, or not.

    The integrated software that uses my Graph Library is called Cytoscape and while still a work in progress is getting way better every release. In terms of the Graphing support, I think we are top notch, but we need to spend more time on algorithms and layouts ;) In addition we have an active development team that is well funded from MSKCC, UCSD, ISB, Agilent, and support from Unilever.

    I will be checking this thread throughout the weekend, so please reply if I can be of more help. And thanks for getting this onto Slashdot! I hope that more people will becocem involved in graphing, and especially in making file formats standard ;)