Search Results for "debian gnu linux" - Page 5
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Showing 225 open source projects for "debian gnu linux"
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A set of very optimized tools for indexing/querying huge genomes/files. Provided so far: a very fast exact mapper, and an unconstrained split-mapper
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The igraph library
Library for creating and manipulating graphs
This is a library for creating and manipulating graphs with focus on speedy operations for large, sparse graphs. -
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GEPETTO - Gene Prioritization in Java
GEPETTO (GEne Prioritization ExTended TOol)
GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein... -
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Application to create 'electronic fluorescent pictographic' representations of gene expression patterns. Created at the Provart lab of the department of Cell & Systems Biology, University of Toronto.
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StabiTissue
3D Stabilization software for intravital imaging of mouse organs
- 2D Stabilization in each slice of the stacks in time. - 3D Stabilization intravital imaging of all the stacks (including the dimension Z) - create the videos and the stabilized images in a new folder -
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SpiKeDeteKt
An automatic spike detection program to be used with new KlustaKwik
This is an automatic spike detection program which takes account of probe geometry and produces a .mask file to be used with the new masked version of KlustaKwik. We recommend you use Python 2.6 or 2.7, e.g. a free academic version can be obtained from Entthought Python. The input files for SpiKeDeteKt are: .dat (raw data file) .probe (probe file, described below - user constructed) parameters.py (optional - otherwise it uses defaultparameters.py) SpiKeDeteKt outputs... -
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The PyCogent project is moving to GitHub. When completed, you will find us at http://github.com/pycogent/pycogent/. You can find the PyCogent website at http://www.pycogent.org.
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Laboratory notebook using version control system and independent date-time stamping (as notarization), in order to ensure record accountability, auditing, and conforming to US FDA 21 CFR 21's rule on electronic records. Please kindly rate this application or drop me an email at [ mauriceling AT acm DOT org ] so that I can hear from you. Otherwise, I have no idea who the users are. Please kindly help.
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CoNIFER
Homepage for CoNIFER (Copy Number Inference From Exome Reads)
CoNIFER uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. -
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Pysimony
A Pythonic Implementation of Parsimony Inference of Phylogeny
UPDATE: After some bug fixes, I've ditched Pysimony for Javamony: https://sourceforge.net/projects/javamony/ Given Python's beauty, I know that someday I will have to finish Pysimony. A student's first attempt at a phylogenetic inference program, written in the simplistic yet elegant Python. Pysimony reads a FASTA file (only ATGC accepted) specified as its only argument. Basic testing has shown that it is slow, inaccurate and most definitely inefficient. An... -
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Primer Design Tool
Design PCR primers
A simple tool to design DNA primers for mutagenesis in BGME lab (JHU). Allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them. -
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pyBioImage
Biological Imaging Software suite
The pyBioImage is a python a python based biological imaging suite tailored to the problem of finding Germinal Center "spots" within multidimensional microscopy images as it is described in the research paper: "Software tool for 3D extraction of germinal centers", by David N. Olivieri, Merly Escalona and Jose Faro. -
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brocc
BLAST Read and OTU Consensus Classifier
NOW HOSTED ON GITHUB: https://github.com/kylebittinger/brocc Old releases are kept here for archival purposes. -
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GemSIM is a software package for generating realistic simulated next-generation sequencing reads with quality score values. Both Illumina and Roche/454 reads (single or paired end) can be simulated using appropriate empirical error models.
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QUASR
Cross-platform NGS processing and analysis pipeline in Python
QUASR is a lightweight pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal demultiplexing primer-removal quality-assurance (QA) graphing quality control (QC) consensus-generation minority-variant determination minority-variant graphing The main current version is 6.X, which is... -
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QDC (quick direct-method controlled) is an optimized exact implementation of the Gillespie's direct-method. It is designed for biochemical simulations when there is the need of dynamic parameters whose values can change during the simulation.
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metaProt
Pipeline to analyze coding regions in metagenomic projects
metaProt is a python pipeline to analyze and extract data from protein sequences found in metagenomic projects. It integrates several existing tools (HMMer, Pepstats, Blast...) to be used against custom databases. Please, read the README.txt file to find more about this. -
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GWCNV is a genome-wide algorithm for detecting CNV associations with diseases. It works directly on a transformation of intensity data. It is powerful and sensitive in detecting small CNV associations, and retains high power for large CNVs.
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We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.
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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.
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NetBuilder' is a tool for building, visualizing, and simulating multi-layered biological networks, structured as hierarchical Petri-nets. It has a built-in stochastic simulator, but also provides easy access to other simulation and analysis.
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Software to identify cavities and crevices in proteins. The goal is to be able to take a protein structure, and to differentiate between five different types of environments for each residue: buried, surface, interfacial, cavity, or crevice.
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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.
