An open source framework for LC-MS based proteomics and metabolomics. OpenMS offers data structures and algorithms for the processing of mass spectrometry data. The library is written in C++.
Several RNA and protein structure volume calculation tools.
RoadRunner represents a state-of-the-art simulation library for SBML models. It is fast, portable and accurate. This projects hosts the library and tools using the library.
Extremely fast NGS read counter
... bam_file(s) > output Requires bamtools API library at run time, and c++0x for compile. git clone https://github.com/pezmaster31/bamtools cd bamtools mkdir build cd build cmake .. make export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:path to/lib g++ -I bamtools/include/ -L bamtools/lib/ -o fast_count_multi fast_count_multi.cpp -lz -lbamtools -fpermissive -pthread -std=c++0x
flexible barcode and adapter removal for sequencing platforms
Flexbar moved to https://github.com/seqan/flexbar The program Flexbar processes high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar supports next-generation sequencing data in fasta and fastq format, e.g. from the Illumina platform. Reference: Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for...
A tool for 3D genome and chromosome structural model construction
Gen3D is an application designed to determine three-dimensional genome and chromosome models. It uses chromosomal contact data to construct three-dimensional conformations. This method can generate three-dimensional chromosomal models satisfying a large portion of chromosomal contacts. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project is...
Elastic network models (ENMs) have been shown to generate the dominant functional equilibrium motions of biomolecules quickly and efficiently. MAVEN simplifies ENM generation, allows for diverse models to be used, and facilitates useful analyses.
The project has moved to GitHub: https://github.com/pixmeo/osirix
We present an improved ball and stick representation called HyperBalls. This type of depiction is particularly useful to represent dynamic phenomena, such as the evolution of non covalent bonds and takes advantage of GPU capabilities. HyperBalls are now fully integrated into the UnityMol software and are actively developed in that context. You will find the most up-to-date versions of the shaders in the http://unitymol.sourceforge.net project.
A C++ Library for modelling and analyzing biochemical networks
EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
EXtensible Instrument Processing Protocol (XIPP) is used to query, configure, and stream data between XIPP-enabled instruments and personal computers on dedicated instrument networks using UDP packets. Cross-platform, C/C++.
This set of C++ classes allows the user to load data from custom Affymetrix microarrays. This is a good platform for new method development and it contains several common normalization algorithms.
The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in structural biology to facilitate the development of molecular modeling, design and analysis tools.
Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)
A C++ development library designed to make common operations on DNA and protein sequences easy. libGenome provides functionality to read, write, and manipulate sequence and annotation data in several file formats.
The Synaptic Simulator is a program which simulates models of single neuronal synapses and compartments, complex constructs of such models. Furthermore the program is able to regain parameters by fitting simulated results with experimental data.
Generic C++ library for the training and evaluation of predictive and classification models from data matrices as used in bio- and chemoinformatics. SiMath provides a simple interface to a broad range of tools like SVM, PCA, SOM, k-means clustering.