Search Results for "language"
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Showing 99 open source projects for "language"
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Systems Biology Markup Language (SBML)
A file format for exchanging computational models in systems biology
The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more. -
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Biological Pathway Exchange Language
A Data Exchange Format for Biological Pathway Information
BioPAX is a standard language for integration, exchange, visualization and analysis of biological pathway data. BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently. -
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Jmol
An interactive viewer for three-dimensional chemical structures.
...Files can be transferred directly from several databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple files can be loaded and compared. A rich scripting language and a well-developed web API allow easy customization of the user interface. Features include interactive animation and linear morphing. Jmol interfaces well with JSpecView for spectroscopy, JSME for 2D->3D conversion, POV-Ray for images, and CAD programs for 3D printing (VRML export). -
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Free DELTA
Software tools for processing taxonomic descriptions in DELTA format
The Free DELTA Project is a free, open-source, software alternative for a generic system to the processing of taxonomic descriptions based on the DELTA (DEscription Language for TAxonomy) format. -
Desktop and Mobile Device Management SoftwareDesktop Central is a unified endpoint management (UEM) solution that helps in managing servers, laptops, desktops, smartphones, and tablets from a central location.
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Open Information Systems for Emergency Services (Open ISES) is a community of software developers, paramedics, EMTs, law enforcement & fire fighters working together to create open source software & training materials for the emergency service community.
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NeuroML is an XML-based description language for defining and exchanging neuronal cell, network and modeling data including reconstructions of cell anatomy, membrane physiology, electrophysiological data, network connectivity, and model specification
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SBEVSL is a collaborative project between Dowling and RIT on the development of a Structural Biology Extensible Visualization Scripting Language, so that users can move freely among various molecular graphics tools, such as rasmol, pymol, raster3d, etc.
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Finding DNA Repeats by RFRE
RFRE is a tool to find DNA repeats (tandem and short)
A tool to FIND DNA REPEATS (tandem and short): RFRE is a mini tool to search for the repeated DNA sequences (SHORT REPEATS OR TANDEM REPEATS) characters by using the regular expression language (VB script). The Metacharcter and their behaviours in the context of regular expressions are the main methods to identify the different searched patterns and by different combination of Metacharcter, the programmed tool can search and detect the pattern of DNA sequence. Repeater Finder Regular Expression Tool Regular Expression for Protein Motif Search and SSR sequence. ... -
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GroIMP
Growth-grammar related Interactive Modelling Platform
...The modelling platform GroIMP is designed as an integrated platform which incorporates modelling, visualisation and interaction. It exhibits several features which makes itself suitable for the field of biological or ALife modelling: The “modelling backbone” consists in the language XL. It is fully integrated, e.g., the user can interactively select the rules to be applied. GroIMP provides classes that can be used in modelling: Turtle commands, further geometrical classes like bicubic surfaces, the class Cell which has been used in the Game Of Life implementation, and so on. The outcome of a model is visualised within GroIMP. ... -
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bioweb
polyglot language framework to analyze genetic data
polyglot framework using Python/C++/JavaScript to fast develop applications to analyze biological sequences -
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Antimony
Antimony is a human-readable, human-writable model definition language
Antimony is a human-readable, human-writable model definition language. libAntimony is a library that will read and write Antimony and SBML files and provides an API for other programs to import Antimony models into their own internal formats. -
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TIES
A smart search engine for medical documents
TIES (Text Information Extraction System) is a clinical text search engine that uses Natural Language Processing techniques to extract medical concepts from free text clinical reports. It provides secure de-identified access to this information and has in built collaboration tools and honest broker functionality. It is licensed for academic use under the BSD license. For commercial use please contact Nexi at http://nexihub.com *** NOTICE: this software and forum are no longer maintained, as of 8/15/2019. ... -
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infix2pharmml
Converter between mathematical infix notation and PharmML math markup.
PharmML is a markup for pharmacometrics markup language documented at http://pharmml.org/. This project provides a converter between the conventional mathematical infix notation and the math markup used by PharmML. The online version has been disabled. Please download for offline use. -
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NanoR
R package built to analyze and compare Nanopore data
NanoR is a package for the statistical language and environment R, tested on Unix, MacOSX and Windows, that allows user-friendly analysis and comparison of 1D MinION and GridION X5 sequencing data within acceptable time frames. -
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N2A
Neurons to Algorithms - A neural modeling and simulation workbench
"Neurons to Algorithms" (N2A) is a language for modeling neural systems, along with a software tool for editing models and simulating them. N2A is currently "alpha" software. The download provided on SF is for convenience to those who wish to preview the software. Please see our site on github for development status. -
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pySBOL
SWIG-Python wrappers for libSBOL
pySBOL is a SWIG-Python wrapper around libSBOL, a module for reading, writing, and constructing genetic designs according to the standardized specifications of the Synthetic Biology Open Language (SBOL). This page provides binary installers for Windows operating system for Python 2.7 and 3.6. For installation instructions, visit: https://pysbol2.readthedocs.io/en/latest/installation.html For full documentation, visit: https://pysbol2.readthedocs.io/en/latest/index.html -
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libSBOL provides the core C/C++ interfaces and their implementation for the Synthetic Biology Open Language (SBOL). Version 2.1.1 of libSBOL provides an API to construct SBOL 2.1.0 designs and to read and write SBOL version 2.1.0 XML/RDF files.
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ABC-SysBio implements likelihood free parameter inference and model selection in dynamical systems. It is designed to work with both stochastic and deterministic models written in Systems Biology Markup Language (SBML).
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GNAT
GNAT recognizes gene names in text and maps them to NCBI Entrez Gene
GNAT is a BioNLP/text mining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID. March 2017: We started to upload GNAT output on Medline. See files/results/medline/. -
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RDML stands for Real-time PCR Data Markup Language and is the standard file format for export, storage and exchange of quantitative PCR (qPCR) data. This project focuses on the development, implementation and enhancement of the RDML file format and its description (XML schema).
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cfPred
Chou & Fasman algorithm implemented using C language.
Chou & Fasman algorithm implemented using C language. It is a CUI tool used for protein secondary structure prediction. -
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The Simulation Experiment Description Markup Language (SED-ML) is a formal representation aimed at encoding requirements defined in the MIASE guidelines. THIS REPOSITORY IS DEPRECATED AND MOVED TO https://github.com/sed-ml
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CuiTools (Coo-e Tools) is a freely available package of Perl programs for unsupervised and supervised word sense disambiguation experiments. The name CuiTools comes from the Concept Unique Identifiers (CUIs) found in the Unified Medical Language System.
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TEES
Turku Event Extraction System
Turku Event Extraction System (TEES) is a free and open source natural language processing system developed for the extraction of events and relations from biomedical text. It is written mostly in Python, and should work in generic Unix/Linux environments. Currently, the TEES source code repository still remains on GitHub at http://jbjorne.github.com/TEES/ where there is also a wiki with more information. -
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BOWS
Bioinformatics Open Web Services
BOWS is a generic system based on Web Services which allows programmatic access to applications running on HPC clusters. BOWS allows incorporation of several independent applications since programmers can install them in HPC clusters in any programming language. The lonely requirement is to write a script named “arrow” which calls BOWS back-end services periodically in order to check for new processes and their required parameters. If a new process is found, the “arrow” script should change the requisition status from waiting to running, run the process in the HPC cluster and, when the job is complete, call a BOWS back-end service to send the results. ...
