SBW - Systems Biology Workbench Portable

Made as the portable edition of SBW - Systems Biology Workbench, this is an application suite that integrates several tools dedicated to app inter-communications, including an inspector module, layout designer, and script-based model editor.

It offers support for several programming and scripting languages, including Java, C++, Perl and Python.

The key difference between this edition and the installer is that you can keep all of SBW Portable's configuration files in a single directory that can be easily deleted afterward. Plus, you can save it to a removable storage unit to directly launch it on any PC without any installers.

All of Systems Biology Workbench's modules can be separately launched. They are wrapped in a user-friendly interface that doesn't put too much emphasis on looks, but it has a neatly organized structure.

SBW Inspector shows services and methods for the BROKER and C# Inspector modules, giving you the possibility to run methods by inputting strings, generate CSV for arrays, preserve CRLF, or use C style escaped strings. You can copy methods to the Clipboard and investigate interface documentation provided by the application.

SBW AutoLayout lets you open and view SBML files, analyze their elements, set the node spacing and level of gravity, specify the center node on the screen, randomize settings, or apply the automatic layout.

It's also possible to examine compartments, forces and control points, use magnetism, boundary or grid, analyze the flux balance and general network, run a general simulation, view the model's Jacobian, translate SMBL into other formats, and so on.

Jarnac is a program for interactive system biology that integrates a Jarnac/SBML editor and chart. You can load simple simulation or steady state templates, disable the socket server, view the class library and history panel, keep an eye on the memory status, as well as customize graphs and save charts to file.

Meanwhile, JarnacLite gives you the possibility to edit SBML, XML and JAN files, export them to PDF format, validate code, customize the font, or change the kinetic law.

JDesigner is a network visual designer which provides you with some intuitive tools for creating projects, like species nodes, compartments, connections, and negative regulators. It's possible to modify the molecule glyph design, edit properties for species, reactions, compartments and regulatory edges, manage parameter sets, copy the design as a bitmap or metafile image, and export images to GraphML, simple or transparent bitmap, metafile, image map, dialog or tikz format.

SMBL Layout Extension Viewer is a simplistic app that lets you load files with SBML layouts or rendering information, in addition to JDesigner, JDesigner 2 or CellDesigner annotations. It can recalculate dimensions, overwrite the layout with SBGN style, change the stylesheet colors, and save data with different extensions than the original, like PNG (with or without transparency), BMP, JPEG and SVG.

Using SBML Translator you can open SBML files to examine code written in SBML, XPP, C, FOTRAN, Jarnac Lite, MatLab, Mathematica, C# and Java (it's instantly translated). Plus, you can edit code and save the new file.

Lastly, the SBW Simulation tool facilitates a user-friendly workspace for running simulation experiments by supplying it with SBML models. It has functions for analysis (frequency, general scan, pulse, rate vs. species, signal injection, structural), scripting (Python), SED-ML, timecourse (stochastic, time course simulation, timecourse continuous), and steady state analysis.

After entering the required parameters, the app generates graphs which can be customized in appearance, saved as images, copied to the Clipboard, or printed. Moreover, you can switch to a different simulator, alter parameters for floating and boundary species along with initial conditions, toggle anti-aliasing mode, manage plugins, and so on.

The application suite worked smoothly in our tests, without hanging, crashing or displaying error messages. Surprisingly, it had a low impact on computer performance.

To conclude, SBW - Systems Biology Workbench comes equipped with comprehensive tools and intuitive options for viewing, designing, analyzing and manipulating quantitative systems biology data. Make sure to arm yourself with patience to explore it.