Abstract

AbstractA cornerstone of systems biology is the use of computational modeling, by which hypotheses can be cast into a quantitative form that can be tested systematically. The use of computational modeling by biologists promises to pave the way for more rigorous analyses of biological functions, and ultimately will lead to new and better treatments for disease.A crucial enabler for more widespread use of computational modeling in biology is reaching agreement on how to represent, store, and communicate models between software tools. The Systems Biology Markup Language (SBML) project is an effort to create a machine-readable format for representing computational models in biology. By supporting SBML as an input and output format, different software tools can operate on the same representation of a model, removing chances for errors in translation and assuring a common starting point for analyses and simulations. SBML has become the most successful effort in this direction so far, with over 100 software systems supporting it today.In this presentation, I will discuss the current state of SBML, including recent developments such as this year's finalization of Version 2 of SBML Level 2. I will also survey some of the software tools that support SBML, and related projects that have arisen to support more effective use of computational models. Lastly, I will discuss expected future developments in SBML.

Highlights

  • Conviction that computational modeling is crucialEnables quantitative hypothesis testingNot a new idea—dates to 1940’s if not earlierTheoretical & technological advances made since Support is better than everGeneral mathematical environmentsSpecial-purpose software toolsSpecialized software tools for computational modeling in biology > 100 availableRange of capabilitiesEditing/creating models

  • SBML development process so far Informal discussions lead to proposals for change

  • Proposals for SBML extensions can come with libSBML add-on

Read more

Summary

Introduction

Conviction that computational modeling is crucialEnables quantitative hypothesis testingNot a new idea—dates to 1940’s if not earlierTheoretical & technological advances made since Support is better than everGeneral mathematical environmentsSpecial-purpose software toolsSpecialized software tools for computational modeling in biology > 100 availableRange of capabilitiesEditing/creating models. Co-director—Biological Network Modeling Center (BNMC), Beckman Institute Not a new idea—dates to 1940’s if not earlier Specialized software tools for computational modeling in biology

Results
Conclusion
Full Text
Paper version not known

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call