SBMLToolbox: an SBML toolbox for MATLAB users

We present SBMLToolbox, a toolbox that facilitates importing and exporting models represented in the Systems Biology Markup Language (SBML) in and out of the MATLAB environment and provides functionality that enables an experienced user of either SBML or MATLAB to combine the computing power of MATLAB with the portability and exchangeability of an SBML model. SBMLToolbox supports all levels and versions of SBML

Software search is not a science, even among scientists: A survey of how scientists and engineers find software

Improved software discovery is a prerequisite for greater software reuse: after all, if someone cannot find software for a particular task, they cannot reuse it. Understanding people’s approaches and preferences when they look for software could help improve facilities for software discovery. We surveyed people working in several scientific and engineering fields to better understand their approaches and selection criteria. We found that even among highly-trained people, the rudimentary approaches of relying on general Web searches, the opinions of colleagues, and the literature were still the most commonly used. However, those who were involved in software development differed from nondevelopers in their use of social help sites, software project repositories, software catalogs, and organization-specific mailing lists or forums. For example, software developers in our sample were more likely to search in community sites such as Stack Overflow even when seeking ready-to-run software rather than source code, and likewise, asking colleagues was significantly more important when looking for ready-to-run software. Our survey also provides insight into the criteria that matter most to people when they are searching for ready-to-run software. Finally, our survey also identifies some factors that can prevent people from finding software

Software that goes with the flow in systems biology

A recent article in BMC Bioinformatics describes new advances in workflow systems for computational modeling in systems biology. Such systems can accelerate, and improve the consistency of, modeling through automation not only at the simulation and results-production stages, but also at the model-generation stage. Their work is a harbinger of the next generation of more powerful software for systems biologists

SBML models and MathSBML

MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation

Software search is not a science, even among scientists: A survey of how scientists and engineers find software

Improved software discovery is a prerequisite for greater software reuse: after all, if someone cannot find software for a particular task, they cannot reuse it. Understanding people’s approaches and preferences when they look for software could help improve facilities for software discovery. We surveyed people working in several scientific and engineering fields to better understand their approaches and selection criteria. We found that even among highly-trained people, the rudimentary approaches of relying on general Web searches, the opinions of colleagues, and the literature were still the most commonly used. However, those who were involved in software development differed from nondevelopers in their use of social help sites, software project repositories, software catalogs, and organization-specific mailing lists or forums. For example, software developers in our sample were more likely to search in community sites such as Stack Overflow even when seeking ready-to-run software rather than source code, and likewise, asking colleagues was significantly more important when looking for ready-to-run software. Our survey also provides insight into the criteria that matter most to people when they are searching for ready-to-run software. Finally, our survey also identifies some factors that can prevent people from finding software

GLAMM: Genome-Linked Application for Metabolic Maps

The Genome-Linked Application for Metabolic Maps (GLAMM) is a unified web interface for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic networks and investigating the construction of novel, transgenic pathways. This simple, user-friendly interface is tightly integrated with the comparative genomics tools of MicrobesOnline [Dehal et al. (2010) Nucleic Acids Research, 38, D396–D400]. GLAMM is available for free to the scientific community at glamm.lbl.gov

SBSI:an extensible distributed software infrastructure for parameter estimation in systems biology

Complex computational experiments in Systems Biology, such as fitting model parameters to experimental data, can be challenging to perform. Not only do they frequently require a high level of computational power, but the software needed to run the experiment needs to be usable by scientists with varying levels of computational expertise, and modellers need to be able to obtain up-to-date experimental data resources easily. We have developed a software suite, the Systems Biology Software Infrastructure (SBSI), to facilitate the parameter-fitting process. SBSI is a modular software suite composed of three major components: SBSINumerics, a high-performance library containing parallelized algorithms for performing parameter fitting; SBSIDispatcher, a middleware application to track experiments and submit jobs to back-end servers; and SBSIVisual, an extensible client application used to configure optimization experiments and view results. Furthermore, we have created a plugin infrastructure to enable project-specific modules to be easily installed. Plugin developers can take advantage of the existing user-interface and application framework to customize SBSI for their own uses, facilitated by SBSI’s use of standard data formats