The Full-text Index Data structure library, libfid for short, is a portable software library for accessing indexed data through a simple C interface. It implements, among others, functions for reading indexed data from files, and for performing common operations such as fast string matching. Easy alphabet handling for mapping between printable and binary alphabets is integrated from the ground up. Currently, the enhanced suffix array is the only full-text index data structure supported. A very simplistic program for constructing enhanced suffix arrays is included.
mkESA is a program for constructing enhanced suffix arrays (ESAs) from biological sequence data. The program is based on an implementation of Manzini's lightweight Deep-Shallow algorithm, which can also utilize multiple CPUs/cores for extra performance. The generated output is compatible with the output of mkvtree from the Vmatch package.
CESE Plus is a software platform designed to perform a wide array of cell electrophysiology simulations. It is a universal simulation environment supporting multitude of cell models and systems, including cardiac atrial, ventricular and SA node models, neuronal models, and more. CESE Plus is an enhanced commercial version of the CESE platform. These enhancements include full support for Mac OS X; a split display for comparison of multiple simulated data traces; data import and export between MS Excel, Axon text files, and ASCII tables; powerful cursors to select regions of interest and perform online measurements and statisical analysis; VirtuClamp to simulate voltage clamp and current clamp protocols; improved equation solvers with greater accuracy; and full commercial support.
GoFigure2 is a cross-platform application for visualization, processing, and analysis of out-of-core multidimensional microscopy data (5D data sets). Users can visualize images, segment cells in 3d, track cells through time, and detect cell divisions to generate lineages. Results are stored in a MySQL database back-end. Once data has been processed, cell-based object features are quantified and can be used for sorting, color-coding, analysis, or exported to external tools. GoFigure2 was developed for biology research including studying the development of embryos (zebrafish and mouse), synthetic biology (signaling), and for drug screening.
PathVisio is a bioinformatics tool that lets you do everything with biological pathway diagrams. PathVisio helps you organize biological information and lets you present or publish that information easily. You can create and draw pathways, export them to many image formats, annotate them with links to online biological databases such as Ensembl, Entrez or HMDB, and add comments and literature references from pubmed. PathVisio also lets you sort through high-throughput experimental data in pathway context. This is a much more pleasant way to present data than just a large table. You can import microarray, proteomics or metabolomics data. PathVisio has a plugin interface that lets users customize it to new analysis types, new visualization methods, and new pathway formats. PathVisio is compatible with WikiPathways.
JHeatChart is a one class Java API for generating heat map charts that was created because very few charting APIs seem to contain the facility to create heat maps. It is not a full featured charting API and cannot be used to other charts. The generated charts are created as Java Image objects, which can be incorporated into a GUI or saved to a file.
LabKey Server is open source software that helps scientists manage, analyze, and share complex datasets. It supports tandem mass spectrometry, flow cytometry, assays for neutralizing antibodies, Luminex, observational studies, and secure, Web-based collaboration. The software is modular, configurable, and customizable. It can be installed in your institution on any modern hardware and operating system. It is designed to integrate with your existing systems, instruments, and work flows, and to be readily adapted by skilled programmers to novel methods of inquiry. The project is under active development by a team of professional software engineers and a community of active contributors. New versions are released about four times per year.