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http://www-huber.embl.de/users/anders/HTSeq/doc/count.html

Script distributed with the HT-Seq Python framework for processing RNA-seq or DNA-seq data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: htseq-count (RRID:SCR_011867) Copy   

•   Source: SciCrunch Registry

http://bioinfo.au.tsinghua.edu.cn/software/RNAseqViewer/

Software to visualize the various data from the RNA-Seq analyzing process, for single or multiple samples.

Proper citation: RNAseqViewer (RRID:SCR_011900) Copy   

•   Source: SciCrunch Registry

http://pages.cs.wisc.edu/~bsettles/abner/

A software tool for molecular biology text analysis. At ABNER''s core is a statistical machine learning system using linear-chain conditional random fields (CRFs) with a variety of orthographic and contextual features.

Proper citation: ABNER (RRID:SCR_011868) Copy   

•   Source: SciCrunch Registry

http://transcriptome.ens.fr/eoulsan/

A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers.

Proper citation: Eoulsan (RRID:SCR_011901) Copy   

•   Source: SciCrunch Registry

http://fx.gmi.ac.kr/

A user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept of cloud-computing.

Proper citation: FX (RRID:SCR_011902) Copy   

•   Source: SciCrunch Registry

http://www.eecs.ucf.edu/~xiaoman/SIOMICS/SIOMICS.html

A software to de novo identify motifs in large sequence datasets such as those from ChIP-seq experiments.

Proper citation: SIOMICS (RRID:SCR_011990) Copy   

•   Source: SciCrunch Registry

http://mga.bionet.nsc.ru/soft/maia-1.0/

Software package of programs for complex segregation analysis in animal pedigrees.

Proper citation: MAIA (RRID:SCR_007153) Copy   

•   Source: SciCrunch Registry

http://www.nybb.hs.columbia.edu/

A brain bank which collects postmortem human brains to meet the needs of neuroscientists investigating specific psychiatric and neurological disorders. NYBB disburses tissue samples to investigating clinicians or scientists whose research has been approved by their Institutional Review Board. The tasks of the NYBB include: collection and processing of human postmortem brain samples for research; neuropathological evaluation and diagnosis; storage and computerized inventory of brain samples; and distribution of brain samples to investigating clinicians and scientists. Brains from individuals without neurological or psychiatric disorders are used as normal controls.

Proper citation: New York Brain Bank at Columbia University (RRID:SCR_007142) Copy   

•   Source: SciCrunch Registry

http://www.alttox.org/

A website dedicated to advancing non-animal methods of toxicity testing, both to better protect the health of humans, animals, and the environment and to reduce the numbers and suffering of animals used in current toxicology assessments. The website is designed to encourage the exchange of technical and policy information on in vitro and in silico methods for all types of toxicity tests. The AltTox Forum is a message board for the AltTox community to use for posting news, information, and perspectives as well as encouraging feedback and commentary. This online community is intended to foster progress internationally in the development, validation, and acceptance of in vitro methods, with the goal of decreasing our reliance on animal-based safety testing. The Forum is moderated by a group of internationally-recognized subject matter experts. The Way Forward invited commentaries, which are posted in the TTRC, are opinion pieces written by experts in each relevant subfield. These essays are meant to help chart the course for future developments by advancing opportunities to overcome challenges and barriers to progress. Stakeholders are invited to comment on these essays in The AltTox Forum. AltTox users are encouraged to contribute to the website and interact with other users in several ways, including: :- Participating in the online forum :- Providing invited expert commentaries :- Suggesting or submitting content, events, monthly features, data, and graphics :- Providing feedback through the Website Feedback surve To encourage objectivity, the website content is overseen by an editorial board of distinguished subject matter experts.

Proper citation: AltTox: Non-animal Methods for Toxicity Testing (RRID:SCR_007212) Copy   

•   Source: SciCrunch Registry

http://www.frontiersin.org

Frontiers community is a web portal for both open access Frontiers journals and a community portal for jobs, books, and scholarly events. Frontiers is more than just an open-access publisher of scholarly articles: it is a pioneering approach to the world of academia, radically improving the way scholarly research is managed. The grand vision of Frontiers is a world where all people have an equal opportunity of seeking, sharing and generating knowledge. As a first active measure in this direction, Frontiers provides immediate and permanent online open access to all of its publications, but this alone is not enough to realize our grand goals. The Frontiers solution develops around two main concepts, mutually integrating each other within the innovative Frontiers'' platform: * the Frontiers Journal Series, and * the Frontiers Community. As an open-access Journal Series, Frontiers revolutionizes research publishing by freely delivering the most outstanding research, evaluated with no bias from both the academic and social point of view. As an interdisciplinary Community system, Frontiers is reshaping research management with a state-of-the-art platform, designed as a collaborative architecture and aimed at all research communities, whether academicians or research enthusiasts, investors or grantmakers. By applying the most advanced information technologies, Frontiers is catapulting scholarly publishing into a new 21st century generation.

Proper citation: Frontiers Community: A Network that Serves researchers (RRID:SCR_007214) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CBO

Ontology that describes multi-cell computational models. In particular to describe both the existential behaviors of cells (spatiality, growth, movement, adhesion, death, ...) and computational models of those behaviors.

Proper citation: Cell Behavior Ontology (RRID:SCR_007055) Copy   

•   Source: SciCrunch Registry

http://www.biomanta.org/

This project encompasses development of novel biological network analysis methods and infrastructure for querying biological data in a semantically-enabled format, and aims to create a semantic interactome model. Research within the BioMANTA project will focus on computational modelling and analysis, primarily using Semantic Web technologies and Machine Learning methods, of large-scale protein-protein interaction and compound activity networks across a wide variety of species. A range of information such as kinetic activity, tissue expression, and subcellular localization and disease state attributes will be included in the resulting data model. Protein interactions are a fundamental component of biological processes. Many proteins are functional only in multimeric complexes, or require interaction partners to achieve their correct localisation or function. For this reason, the study of protein-protein interaction (PPI) networks has become an area of growing interest in computational biology. Through the use of Semantic Web technologies such as Resource Description Framework (RDF) and Web Ontology Language (OWL), interaction data is modelled to create a knowledge representation in which meaning is vested in the ontology rather than instances of data. Stochastic and computational intelligence methods are applied to this data to infer high coverage networks. Semantic inferencing is used to infer previously unknown and meaningful pathways. Major project components: - The BioMANTA Ontology:- An OWL DL ontology incorporating the PSI-MI Ontology, the NCBI Taxonomy, and elements of BioPax ontology and Gene Ontology (describing subcellular localisation). This allows us to re-use existing ontologies, thereby reducing overheads associated with knowledge acquisition in the ontology development process. We are able to integrate existing public data that contain annotation in these formats. - Data conversion & semantic protein integration:- A set of software components that convert protein-protein databases (DIP, MPact, IntAct, etc.) from PSI-MI XML to RDF compliant with the BioMANTA ontology. These software allow us to make these protein-protein interaction datasets (and more generally, any PSI-MI XML data) semantically available for querying and inference within BioMANTA. - A RDF triple store based on RDF Molecules and the MapReduce architecture:- A proof-of-concept RDF triple store using RDF molecules and Hadoop scale-out architectures. Regular RDF graphs are deconstructed into RDF molecules, which are distributed over distributed compute nodes in the MapReduce architecture, and are subsequently combined to form equivalent RDF graphs. Such an approach makes the distributed SPARQL querying and reasoning on RDF triple stores possible. - A quantitative framework to integrate networks extracted from independent data sources (gene expression, subcellular localization, and ortholog mapping):- The model is multi-layer, with a first layer based on Decision Trees where each Decision tree is built on each dataset independently. The tree nodes are cut using Shannon''s entropy (mutual information); the decision of these independent trees is integrated using logistic regression, and the parameters are optimised using maximum likelihood. Sponsors: This resource is supported by the Pfizer Global Research and Development, the Institute for Molecular Bioscience (IMB), and the University of Queensland, Australia.

Proper citation: BioMANTA (RRID:SCR_007177) Copy   

•   Source: SciCrunch Registry

http://www.bioscreen.fi

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 18,2025. Biosceen C is a system designed for automating routine microbiology work. It uses a unique micro-plate format (10x10 wells), so called Honeycomb format, which is especially well suited for highly accurate temperature control. It features two covered honeycomb plates making it possible to run 200 samples simultaneously. Its unique patented incubator system features temperature control maintaining the set temperature with a 0,1 degree centigrade accuracy, while avoiding condensation of liquid on the inside of the micro plate lid. It can cool down the samples 6 degrees centigrade below the ambient temperature and its working range is from 1 to 60 degrees in steps of 0,1 degree centigrade. Sponsors: Oy Growth Curves Ab Ltd is a privately held company established in 2002 by a former Labsystems executive. It aquired the Bioscreen product line from Thermo Labsystems and has continued to maintain the product excellence Bioscreen is known for. Today the company is controlled by a new generation of owner operators, dedicated to continue developing Bioscreen to meet the demands of today''s users Keywords: Microbiology, Automation, Honeycomb, Incubation, System, Temperature, Technology, Supplier,

Proper citation: Bioscreen: C MBR (RRID:SCR_007172) Copy   

•   Source: SciCrunch Registry

http://humancyc.org/

The HumanCyc database describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional analysis of Homo sapiens at the genomic level. A computational pathway analysis of the human genome assigned human enzymes to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary step toward quantitative modeling of metabolism. HumanCyc contains the complete genome sequence of Homo sapiens, as presented in Build 31. Data on the human genome from Ensembl, LocusLink and GenBank were carefully merged to create a minimally redundant human gene set to serve as an input to SRI''s PathoLogic software, which generated the database and predicted Homo sapiens metabolic pathways from functional information contained in the genome''s annotation. SRI did not re-annotate the genome, but worked with the gene function assignments in Ensembl, LocusLink, and GenBank. The resulting pathway/genome database (PGDB) includes information on 28,783 genes, their products and the metabolic reactions and pathways they catalyze. Also included are many links to other databases and publications. The Pathway Tools software/database bundle includes HumanCyc and the Pathway Tools software suite and is available under license. This form of HumanCyc is faster and more powerful than the Web version.

Proper citation: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism (RRID:SCR_007050) Copy   

•   Source: SciCrunch Registry

http://brainatlas.mbi.ufl.edu/Database/

Comprehensive three-dimensional digital atlas database of the C57BL/6J mouse brain based on magnetic resonance microscopy images acquired on a 17.6-T superconducting magnet. This database consists of: Individual MRI images of mouse brains; three types of atlases: individual atlases, minimum deformation atlases and probabilistic atlases; the associated quantitative structural information, such as structural volumes and surface areas. Quantitative group information, such as variations in structural volume, surface area, magnetic resonance microscopy image intensity and local geometry, have been computed and stored as an integral part of the database. The database augments ongoing efforts with other high priority strains as defined by the Mouse Phenome Database focused on providing a quantitative framework for accurate mapping of functional, genetic and protein expression patterns acquired by a myriad of technologies and imaging modalities. You must register First (Mandatory) and then you may Download Images and Data.

Proper citation: MRM NeAt (Neurological Atlas) Mouse Brain Database (RRID:SCR_007053) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/

Our research group develops and applies computational techniques for modeling and understanding biological processes at the molecular level. Our research emphasizes the application of statistical and machine learning techniques, such as hidden Markov models and support vector machines. We apply these techniques to various types of biological data, including DNA and protein sequence data, as well as gene expression data from microarray experiments. We are currently developing methods for analyzing shotgun proteomics data, for characterizing protein function, structure and interactions, and for understanding the structure and regulatory influence of chromatin.

Proper citation: Noble Research Lab (RRID:SCR_007204) Copy   

•   Source: SciCrunch Registry

http://www.ch.embnet.org/software/BOX_form.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. This server takes a multiple-alignment file in either GCG''s MSF-format or Clustals ALN-format. Sponsors: This resource was supported by the Swiss EMBnet Node Server. Keywords: Server, Multiple-alignment,, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BOXSHADE 3.21 (RRID:SCR_007165) Copy   

•   Source: SciCrunch Registry

http://www.aspergillusflavus.org

This is a Research Community that is focused on reducing the threat of the Aspergillus flavus fungus and its toxin to human and animal health. Aspergillus flavus is a plant, animal, and human pathogen that produces the carcinogen, aflatoxin. An organized multidisciplinary team is coordinating research efforts to control this fungus and to prevent the formation of its toxin in food and feeds. Aspergillus flavus is a fungus. It grows by producing thread like branching filaments known as hyphae. Filamentous fungi such as A. flavus are sometimes called molds. A network of hyphae known as the mycelium secretes enzymes that break down complex food sources. The resulting small molecules are absorbed by the myceilium to fuel additional fungal growth. The unaided eye cannot see individual hyphae, but dense mats of mycelium with conidia (asexual spores) often can be seen. The ear of maize below shows the growth of the fungus covering four maize kernels. When young, the conidia of A. flavus appear yellow green in color. As the fungus ages the spores turn a darker green. Sponsors: This resource is supported by the Center for Integrated Fungal Research. Keywords: Aspergillus flavus, Research, Fungus, Toxin, Human, Animal, Health, Plant, Pathogen, Carcinogen, Aflatoxin, Food, Feed, Mold, Network, Enzyme,

Proper citation: Aspergillus Flavus and Aflatoxin (RRID:SCR_007200) Copy   

•   Source: SciCrunch Registry

http://www.soros.org/openaccess/

The purpose of the Budapest Open Access Initiative was to accelerate progress in the international effort to make research articles in all academic fields freely available on the internet. The participants represented many points of view, many academic disciplines, and many nations, and had experience with many of the ongoing initiatives that make up the open access movement. In Budapest they explored how the separate initiatives could work together to achieve broader, deeper, and faster success. They explored the most effective and affordable strategies for serving the interests of research, researchers, and the institutions and societies that support research. Finally, they explored how OSI and other foundations could use their resources most productively to aid the transition to open access and to make open-access publishing economically self-sustaining. The result is the Budapest Open Access Initiative. It is at once a statement of principle, a statement of strategy, and a statement of commitment. The initiative has been signed by the Budapest participants and a growing number of individuals and organizations from around the world who represent researchers, universities, laboratories, libraries, foundations, journals, publishers, learned societies, and kindred open-access initiatives. We invite the signatures, support, and participation of the entire world scientific and scholarly community.

Proper citation: Budapest Open Access Initiative (RRID:SCR_007163) Copy   

•   Source: SciCrunch Registry

http://202.97.205.78/epidiff/QDMRTutorial.jsp

Software that provides a quantitative approach to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy.

Proper citation: QDMR (RRID:SCR_007162) Copy   

•   Source: SciCrunch Registry