CellDesigner: a process diagram editor for gene-regulatory and biochemical networks

Abstract

Context is critical if researchers need toknow the specificity or responsiveness of atarget within a pathway.This is somethingthat has yet to be captured by anyinformatics system,but it will invariably betied to greater utility and even IP definitionsin the near future.To a large extent,pathways data and knowledge managementare seen to go hand in hand,both being usedto make important decisions,and bothrelying on context.It is interesting toconsider that perhaps we are witnessing theemergence of a new informatics paradigm,where knowledge becomes a formallydefined and well-shared scientific andeconomic asset.The third topic that was discussed by afew was the development of new ITstrategies to improve informaticsinfrastructure within large companies.Several speakers presented new andeffective methodologies to design and buildcomplex informatics systems that willeventually become the backbone of drugdiscovery platforms.Richard Ashe describedaccelerated software development programswithin GSK (http://www.gsk.com/) that canadapt more effectively to changing discoveryrequirements.Using lightweightmethodologies and web-based servicesrather than monolithic designing principles,projects could be defined and completedfaster within an ever-changing world ofneeds.Roy Dunbar,CIO of Eli Lilly(http://www.lilly.com/) proposes moreeffective collaborations between IT andscientists to create applications that havemore utility.Juergen Seega from AbbottLaboratories (http://abbott.com/) described‘keeping the scientific and IT worlds in sync’,rather than at odds.Taken together,IT isprogressing from being hidden in thebackwaters of software tinkering,tobecoming a major strategic partner withindrug discovery environments.Other issues were addressed,includinggood laboratory practices as related toinformatics,electronic notebooks,intelligent storage and use of high-throughput screening data,and IP portfoliomanagement.Based on the presentations atthe conference,it was clear that theapplications and benefits of informatics forthe pharmaceutical industry are growing,and that informatics promises to be a keyfactor for the future success of drugdiscovery.Systems biology is characterized by synergisticintegration of theory,computational modeling,and experiment [1].Although softwareinfrastructure is one of the most crucialcomponents of systems biology research,there has been no common infrastructureor standard to enable integration ofcomputational resources.To solve thisproblem,the Systems Biology MarkupLanguage (SBML) [2] and Systems BiologyWorkbench (SBW) have been developed[3].SBML is an open,XML-based format forrepresenting biochemical reaction networks,and SBW is a modular,broker-based,message-passing framework for simplifiedintercommunication between applications.Several simulation and analysis softwarepackages already support SBML (Level-1)and SBW,or are being developed to supportthem.Identification of the logic and dynamics ofgene-regulatory and biochemical networks isa major challenge of systems biology.Webelieve that such network building tools andsimulation environments using standardizedtechnologies play an important role in thesoftware platform of systems biology.As onesuch approach,we have developedCellDesigner,a process diagram editor forgene-regulatory and biochemical networks.In the following,we will introduce themain features of CellDesigner.The mostcrucial elements are that it is a system ofBIOSILICO Vol.1, No.5 November 2003