Search Results for "knowledge"
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Showing 34 open source projects for "knowledge"
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Biological Pathway Exchange Language
A Data Exchange Format for Biological Pathway Information
...In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge. The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap. -
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Collaborative Computing Project for NMR
Collaborative Computing Project for NMR (CCPN)
The Collaborative Computational Project for NMR (CCPN) provides tools and knowledge to maximise the impact of the biological NMR studies. The CCPN software facilitates data analysis and software integration. The project actively promotes the exchange of knowledge and provides training and best practices for the NMR community. CCPN also has a leading role in the development of a NMR data-sharing standard and coordination of NMR instrumentation proposals for RCUK and BIS. ... -
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PDBManip
PDBManip is a free program for editing PDB (Protein Data Bank) Files
...However, in developing PDBManip, I have customized scripting language, by adding predefined PDB related variables and functions, in such a way that a user with a very basic knowledge of programming can easily write very eligible scripts, even for very complicated editing and manipulating tasks. In this way, proficiency in computer programming, that is a must in using Awk or Perl, is not a barrier. -
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P3BSseq
Parallel processing pipeline for analysis of bisulfite sequencing data
...We optimized the P3BSseq parameters for both directional and non-directional libraries, and for both single-end and paired-end reads of Whole Genome and Reduced Representation BSseq. P3BSseq is a user-friendly streamlined solution for BSseq upstream analysis, requiring only basic computer and NGS knowledge. -
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Acacia
A generic biodiversity database management system
An interactive data entry, querying, and editing system based on a generic conceptual schema for taxonomic databases. It combines the automated use of scientific names and synonyms in a species checklist with online access to geographical data and common knowledge data (morphological descriptors, genomics, ecology, vernacular names, economic uses, structured notes and conservation status) about the species. All these data can be cross-indexed to a citation list. The design and standard permits rapid customization to suit any taxonomic group. -
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ExSTraCS
Extended Supervised Tracking and Classifying System
This advanced machine learning algorithm is a Michigan-style learning classifier system (LCS) developed to specialize in classification, prediction, data mining, and knowledge discovery tasks. Michigan-style LCS algorithms constitute a unique class of algorithms that distribute learned patterns over a collaborative population of of individually interpretable IF:THEN rules, allowing them to flexibly and effectively describe complex and diverse problem spaces. ExSTraCS was primarily developed to address problems in epidemiological data mining to identify complex patterns relating predictive attributes in noisy datasets to disease phenotypes of interest. ... -
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SeqSelector
Tools to select sequences for capture enrichment of next-gen libraries
The SeqSelector toolset is a suite of user-friendly, platform independent python scripts to facilitate selection of sequences for targeted enrichment of next-generation libraries through hybridization-based sequence capture. The scripts require no knowledge of programming, and can be applied to genome sequences of model or non-model species. We suggest a workflow in which genes of interest are first identified from previous studies and publicly available datasets of functional gene annotation. Once a list of candidate genes has been identified, their sequences are selected from the reference genome. ... -
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Genomic Binding Sites Analyser (BiSA)
Genomic Region Archiving and Binding Sites Analysis (BiSA)
...BiSA can also annotate binding regions of interest with nearby genes. The results of overlap analysis can be imported into the Knowledge Base, allowing them to go into downstream analysis and independent annotation. A Venn diagram tool is also integrated into the software to allow users to visualize overlap results. -
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CytoCopteR
A Cytoscape plug-in for training logic models, based on CellNOptR.
Homepage: www.cellnopt.org Based on prior knowledge networks CellNOptR can derive functional information about the network using logic modeling. CytoCopteR is a friendly way to use CellNOptR taking advantage of the network visualization and analysis of Cytoscape and without requiring knowledge on R. -
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Bayesian Network tools in Java (BNJ) is an open-source suite of software tools for research and development using graphical models of probability. It is published by the Kansas State University Laboratory for Knowledge Discovery in Databases (KDD).
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VSMOExp
Ontologies, which are made up by standardized and defined controlled
Ontologies, which are made up by standardized and defined controlled vocabulary terms and their inter-relationships, are comprehensive and readily searchable repositories for knowledge in a given domain -
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Ontology Design Patterns (ODPs) are well known and efficient modeling solutions for ontologies. This public catalog offers a collection of well documented and tested ODPs, including examples from the biological knowledge domain, implemented in OWL.
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Clinical Evidence Detector
Detector of clinical evidence
...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 -
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IMAS is a Visual Analytics system for the discovery of knowledge in genomic information. IMAS enables genomic scientists to rapidly analyze and visualize a set of microbial genomic sequences using tools such as Glimmer, Blast, Clustal-W, Primer3.
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FunctSNP is an R interface to an SQL database for linking single nucleotide polymorphisms (SNPs) to functional knowledge. FunctSNP should work on any OS on which R runs.
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OmicBrowse, developed with Flash and Java, is a highly evaluated genome browser integrating omics knowledge ranging from genomes to phenomes and is especially appropriate for positional-cloning purposes.
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BCAR is a library for the associative classification, which denotes "Boosting Class Association Rules". BCAR provides a general tool for classification tasks with various types of input data.
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This software is a GIS, they permit contextualize the information and the extrapolation of knowledge. Permit to calculate the distribution of blood donors and cross reference this with the places of collect.
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Clad organizes a tree of biological species, allowing the user to add scientific and popular names, origin, distribution, apomorphies and other information such as pictures or if the clade is extinct. Browsing through the trees is easy and educative.
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Mathematics, Chemistry and Bio-informatics semantic knowledge editor and simulation environment. It should serve as interactive science learning program or science classroom notebook and workshop.
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The Cell Cycle Ontology extends existing ontologies for cell cycle knowledge building a resource that integrates and manages knowledge about the cell cycle components and regulatory aspects in OBO, OWL, and other commonly used ontology representation
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Protege is a free, open-source platform that provides a suite of tools to construct domain models and knowledge-based applications with frame-based and Semantic Web ontologies.
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Extraction of binding sites of ligands and search for unknown binding sites on apoproteins. Some call it docking. Some call it binding site detections. Some call it knowledge based.
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ASKGene (Automated Sequence Knowledge GENErator) - a customizeable integration platform for sequence-processing bioinformatics tools.
