R is a language and environment for statistical computing and graphics. It is similar to S, which was developed at Bell Laboratories by John Chambers et al. It provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc.). R is designed as a true computer language with control-flow constructions for iteration and alternation, and it allows users to add additional functionality by defining new functions. For computationally intensive tasks, Fortran and C code can be linked and called at run time.
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Wandora is a general purpose data extraction, management, and publishing application based on Topic Maps and Java. Wandora has a graphical user interface, layered presentation of knowledge, several data storage options, rich data extraction, import and export capabilities, and an embedded HTTP server that enables dynamic publication of Topic Maps. Wandora is well suited for rapid ontology construction and knowledge mashups.
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PLOTICUS is a command line utility for creating bar, line, pie, boxplot, scatterplot, sweep, heatmap, vector, timeline, Venn diagrams, and other types of charts and plots. ploticus is good for automated or just-in-time graph generation. It handles date, time, and categorical data nicely, and has some basic statistical capabilities. It can output to GIF, PNG, SVG, SWF, JPEG, PostScript, EPS, and X11. You can use convenient preset options or create complex scripts with rich and detailed color and style operations.
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The Biochemical ALgorithms Library (BALL) is a
framework for rapid application development in
molecular modeling and structural bioinformatics.
BALL provides an extensive set of data structures
as well as classes for molecular mechanics,
advanced solvation methods, comparison and
analysis of protein structures, file
import/export, NMR shift prediction, and
visualization. Its extensibility results from an
object-oriented and generic programming approach.
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MCL-edge is an integrated command-line driven workbench for large scale network analysis. It includes programs for the computation of shortest paths, diameter, clustering coefficient, betweenness centrality, and network shuffles. A module for loading and analyzing gene expression data as a network is provided. The MCL algorithm is a fast and highly scalable cluster algorithm for networks based on stochastic flow. The flow process employed by the algorithm is mathematically sound and intrinsically tied to cluster structure, which is revealed as the imprint left by the process. The threaded implementation has handled networks with millions of nodes within hours and is widely used in the fields of bioinformatics, graph clustering, and network analysis.
The libmba package is a collection of mostly independent C modules potentially useful to any project. There are the usual ADTs including a linkedlist, hashmap, pool, stack, and varray, a flexible memory allocator, CSV parser, path canonicalization routine, I18N text abstraction, configuration file module, portable semaphores, condition variables, and more. The code is designed so that individual modules can be integrated into existing codebases rather than requiring the user to commit to the entire library. The code has no typedefs, few comments, and extensive man pages and HTML documentation.
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Redet is a tool for developing and executing regular expressions using any of more than 50 search programs, editors, and programming languages, intended both for developing regular expressions for use elsewhere and as a search tool in its own right. For each program in each locale, a palette showing the available constructs is provided. The properties of each program are determined by runtime tests, which guarantees that they will be correct for the program version and locale. Additional features include persistent history, extensive help, a variety of character entry tools, and the ability to change locale while running. Redet is highly configurable and fully supports Unicode.
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Engauge Digitizer is digitizing software that converts an image showing a graph or map into numbers. The image file can come from a scanner, digital camera, or screenshot. The numbers can be read on the screen, and written or copied to a spreadsheet. Highlights for beginners include an intuitive interface and extensive context-sensitive documentation. Highlights for experts include compensation for image distortion, cartesian and polar coordinates, linear and logarithmic coordinates, automatic scanning, graphical previews, and browser help.
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SHOGUN is a machine learning toolbox whose focus is on large scale kernel methods and especially on Support Vector Machines (SVM). It provides a generic SVM object interfacing to several different SVM implementations, all making use of the same underlying, efficient kernel implementations. Apart from SVMs and regression, SHOGUN also features a number of linear methods like Linear Discriminant Analysis (LDA), Linear Programming Machine (LPM), (Kernel) Perceptrons, and algorithms to train hidden Markov models. SHOGUN can be used from within C++, Matlab, R, Octave, and Python.
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openModeller is a C++ framework providing tools and an API for ecological niche modeling using a variety of algorithms. It can be used to predict species potential distribution based on a set of georeferenced occurrence points and a set of environmental layers.
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Pathomx is a workflow-based tool for the analysis of metabolomic and other omics datasets. It is interactive, visual, extensible, intelligent, and free for any use. It lets you dynamically build analysis workflows using the interactive editor. Drag and drop connections between plugin tools to create a complete workflow through which to run your analysis. Data can be loaded and processed automatically, and new approaches tested simply by connecting tools.
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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.
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Bioperl is set of Perl Modules for bioinformatics. It contains objects for Sequences, features on Sequences, and other important bioinformatics attributes.
SimThyr is a continuous simulation program for pituitary-thyroid feedback control. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses, and patients.
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AntFlow builds upon Apache Ant to provide a new
approach to simplifying system automation that
uses pipelines of hot folders chained together to
perform a given task. Using XML, it associates an
automated task such as data transfer, encryption,
or XML processing with a directory on the local
system. Whenever a file is copied or written into
the hot folder, the associated task is executed
and the file is moved to the next hot folder in
the pipeline for further processing.
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