Search Results for "bio toolkit"
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Showing 71 open source projects for "bio toolkit"
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Our visitor management system streamlines registration, check-in, and authorization processes, while our facility management tools streamline room booking, resource allocation, and asset management. We prioritize security with our advanced risk mitigation measures, including health and safety protocols, emergency messaging, and robust analytics for thorough auditing.
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aramultiomics
A toolkit for studying protein-protein/nucleic acid interaction
araMultiOmics consisted of seven modules where each module was created based on existing databases and software for studying protein binding sites/open chromatin regions, DNA-TF bonding profile, etc -
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CyberUnits
Class library for computational cybernetics
CyberUnits is a cross-platform class library for rapid development of high-performance computer simulations in life sciences. It supports modelling for biomedical cybernetics and systems biology with Object Pascal. -
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Open Drug Discovery Toolkit (ODDT)
Modular and comprehensive toolkit for use in cheminformatics
Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc. ODDT is written in Python, and makes extensive use of Numpy/Scipy. You can use any supported toolkit united under common API (for reference see Pybel or Cinfony). All methods and software based on Pybel/Cinfony should be drop-in compatible with ODDT toolkits. In contrast to its predecessors, which were aimed to have minimalistic API, ODDT introduces extended methods... -
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APBS
Biomolecular electrostatics software
This software has moved to http://www.poissonboltzmann.org/. -
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An alignment-free standalone tool with interactive graphical user interface for DNA sequence comparison and analysis
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Tissue Simulation Toolkit is a two-dimensional library for the Cellular Potts Model (Graner and Glazier 1992; Phys. Rev. Lett. 69, 2013), which is increasingly used by computational biologists to study tissue patterning and developmental mechanisms.
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Genobuntu
Genobuntu Package for Next Generation Sequencing
Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build ... -
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BisSNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
Now in Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other... -
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ImagingAnalysis
Direct tissue-level image quantification package for Mathematica
ImagingAnalysis is a Mathematica package that performs grid-based analysis of time-lapse imaging data saved in a sequence of TIFF files. This package requires Mathematica 7.0. Revised on 14 May 2017: Bugs are fixed and incompatibility issues are resolved. The current version runs on Mathematica 11. -
ProcureDesk is an integrated purchasing and invoicing platform tailored to help small to medium sized businesses streamline their procurement processes. This user-friendly system automates workflows and consolidates purchasing data into a centralized dashboard, allowing companies to control spending and enhance transparency efficiently. Features like automated invoice matching, simple requisition creation, and immediate cash flow insights minimize manual tasks and boost operational efficiency. ProcureDesk is perfect for smaller enterprises leveraging big-business strategies to reduce costs and optimize their purchasing activities. Discover how ProcureDesk can transform your procurement process into a more effective and manageable part of your business.
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Crux-Toolkit
Software toolkit for tandem mass spectrometry analysis
Crux is a software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification. If you use Crux in your research, please cite Christopher Y. Park, Aaron A. Klammer, Lukas Käll, Michael J. MacCoss and William Stafford Noble. "Rapid and accurate peptide identification from tandem mass spectra." Journal of Proteome Research. 7(7):3022--3027, 2008. -
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Barracuda is a high-speed sequence aligner based on Sanger's BWA and utilizes the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by next-generation sequencers.
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The Maltcms - Modular Application Toolkit for Chromatography Mass-Spectrometry is a JAVA API for preprocessing, alignment, analysis and visualization of data stored in open file formats used in Proteomics and Metabolomics research.
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KAnalyze
DNA/RNA Sequence K-mer Toolkit
KAnalyze is a Java toolkit designed to convert DNA and RNA sequences into k-mers. It is both a command line application and an API. -
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Bamformatics
Toolkit and GUI for sequencing data analysis
The Bamformatics project aims to provide a coherent and consistent approach to analysis of high-throughput sequencing data. Its toolkit includes, among others, programs to identify variants and to compute various types genomic tracks. It also provides a graphical user interface to facilitate general bioinformatic workflows. The project wiki contains further details. -
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Toolkit for processing genetic data. Currently supports (command-line): Half-IBD (Identity by descent) aka HIRs - between 2 or any number of files (in distances and cM); RAW2PED, PED2RAW conversions; regions of homozygousity and other converters.
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TinkerCell is a software for synthetic biology. The visual interface allows users to design networks using various biological "parts". Models can include modules and multiple cells. Users can program new functions using C or Python. www.tinkercell.
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HTQC
Quality control and filtration for illumina sequencing data
A toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc.. -
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openSEQ
NGS compute distro proloaded with pipeline analysis software
.... The first homepage tab links to our pipeline constructer. The second homepage tab links to a xterm session on the client. Software included (location - name): path - biobambam path - bwa path - bowtie2 path - bowtie path - cufflinks path - bcftools path - tophat path - scalpel path - samtools path - sra-toolkit path - bamtools path - delly path - delly-parallel path - picard-tools path - fastahack path - twoBitToFa ~/prog/java/ - mutect ~/prog/python/ - platypus ~/prog/java/ - gatk -
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Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution.
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QUASI is a toolkit to rapidly assess the quality of shRNA-Seq based data and call differential abundance using common statistical inference methods (DESeq, edgeR, baySeq).
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Coulson Plot Generator
Graphics generator for pie diagram matrix from spreadsheets
For comparative plus/minus spreadsheet data, Coulson Plot Generator application creates a multiple pie diagram, for a rapid visual comparison of subunit occupancy across a range of entities. Numbers of pies, segments, labels and colours are customisable. Creates an editable PDF from a comma separated text file. Now with zoom capability and more memory, for larger datasets. Save images in several formats including SVG. -
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The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.
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Gene Ontology Browser
Browser for viewing Gene Ontology (GO) .obo files.
Go Browser allows you to view a gene ontology on your local machine. You can go up and down the hierarchy and inspect the terms. It's a good way of familiarising yourself and orienting yourself in the GO system. It's built using the Baby X toolkit, so has no dependencies other than xlib. Baby X has now also been ported to Windows, so a Windows version is available. -
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SPADE
A toolkit for developing and deploying protein structure algorithms.
The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available. SPADE source code can be cloned from http://www.github.com/deaconjs/SPADE. -
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AJT is a set of utility classes for Java for handling some bioinformatics data, graphics file export, GUI widgets, and classes that should long have been added to the official Java API.