Search Results for "c source code" - Page 17

Turn genes into rhythm. Feed the software with a nucleotide sequence as input, and it will translate it as MIDI messages, designed especially for the KORG ESX-1 but ready to be used with any MIDI-enabled device or software.

GoFigure2 is an open-source, cross-platform application for visualizing, processing and analyzing of multidimensional microscopy data. Users can visualize, segment and track cells through time, detect cell-division and ultimately generate lineages.

Detection of structural variants and indels from Genome/Exome sequencing data

Displays mummer/nucmer mappings and prints PNG to stdout via the "show-coords -lcdTH" output. The output file is <coords-output>.png. Command line options allow for different features when producing the image. Within the code there are comment blocks which give examples of how to further customize it i.e. grouping based on name similarity, color, etc. This program is aimed at providing full customization within the limits of the Bio-Graphics module. Current version supported is Bio-Graphics-2.25

A bioinformatics tool to identify and remove rRNA sequences from metagenomic and metatranscriptomic datasets. The rRNA-like sequences are classified by domain, subunit. and bacterial phyla. Coverage plots for the top hits are provided as well.

ZORRO is a probabilistic masking program that assigns confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines.

Diva is a command-line tool for dispersal-vicariance analysis, a simple method for inferring the distributional history of organisms (Ronquist, F. 1997. Systematic Biology 46:193-201).

This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text. The method is based on SVM but other ML algorithms can be adopted. The method details are explained in the...

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.

BpMatch is an algorithm that, given 2 strings S and T, compute the maximum coverage of T using only subequence or reversed complemented subsequences of S, of minimum length l.

A Generalized Combinatorial Approach for Detecting Gene-by-Gene and Gene-by-Environment Interactions

This is a Python program based on the NegEx algorithm that detects the polarity of the clinical evidence in clinical random trials. If you use this code please cite this paper: P. Davis-Desmond and Diego Mollá. Detection of Evidence in Clinical Research Papers (2012). Australasian Workshop On Health Informatics and Knowledge Management (HIKM 2012), Melbourne, Australia. http://www.ics.mq.edu.au/~diego/publications/hikm12.pdf

BFAST facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance.

This is a c-library that provides tools for advanced analysis of electrophysiological data. It features denoising, unsupervised classification, time-frequency analysis, phase-space analysis, neural networks, time-warping and more.

Set of iterative filters.

ESMERALDA is a development environment for statistical recognizers operating on sequential data (speech, handwriting, biological sequences). It supports continuous density Hidden Markov models, Markov chain (N-gramm) models, and Gaussian mixture models.

A Sequenced Binaural Wave Generator for Linux+Windows. May be used to generate sounds that entrain the brain's waves to oscillate at selected frequencies to aid in relaxation, lucid dreaming, meditation, clear thought, out-of-body experiences + more

The transcriptome analyser project aims to provide tools to determine and document all the transcribed parts of a genome. The transcribed parts are defined by analysing experimental evidence, like expressed sequence tags (EST) and other mRNA sequences.

As an NIAID Bioinformatics Resource Center (BRC) Pathema contains in depth curatorial analysis of six target organisms from the list of NIAID category A-C pathogens. Pathema also offers single-genome and comparative multi-genome analyses as well as displ

ODD is a tool for optimal domain decomposition of atomic structure guided by the given molecular dynamics data.

Web application to make user-friendly requests on large XML database. Tools to XML-ize large bodies of semi-formal texts (like floras). Computer-assisted specimen identification. Uses natural language processing, 2D/3D images analysis and generation.

Biologic Institute's Stylus simulation software suite. (See the SVN repository for source code.)

A set of command-line utilities for annotating and manipulating DNA sequences in FASTA format. Generate restriction fragments, ORF's, translations, reverse complement, etc. . - and tie it all together with Unix pipes for complete virtual cloning.

CellNet3D is an application for visualising chemical formula in 3D on Linux platform through PDBlib and X11.

Metaboflux is a generic approach for predicting flux distribution in metabolic networks under multiple and various constraints deducted from the experiments, to increase the biological relevance of the model.