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http://www.neurophys.biomedicale.univ-paris5.fr/~graham/surf-hippo.html

The Surf-Hippo neuron simulator is used to investigate morphologically and biophysically detailed compartmental models of single neurons and networks of neurons. Surf-Hippo allows ready construction of cells and networks using built-in functions and various anatomical file formats (Neurolucida, NTS and others). Surf-Hippo is a public domain package, written in Lisp, and runs under Unix and Linux.

Proper citation: The Surf-Hippo Neuron Simulation System (RRID:SCR_007257) Copy   

•   Source: SciCrunch Registry

http://www.autopack.org/

A specialized version of autoPack designed to pack biological components together. The current version is optimized to pack molecules into cells with biologically relevant interactions to populate massive cell models with atomic or near-atomic details. Components of the algorithm pack transmembrane proteins and lipids into bilayers, globular molecules into compartments defined by the bilayers (or as exteriors), and fibrous components like microtubules, actin, and DNA.

Proper citation: Cellpack (RRID:SCR_006831) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/soapaligner.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Updated version of SOAP software for short oligonucleotide alignment that features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAPaligner/soap2 (RRID:SCR_005503) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/LONI-Inspector

A Java application for reading, displaying, searching, comparing, and exporting metadata from medical image files: AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI.

Proper citation: LONI Inspector (RRID:SCR_004923) Copy   

•   Source: SciCrunch Registry

http://snap-graph.sourceforge.net

SNAP (Small-world Network Analysis and Partitioning) is an extensible parallel framework for exploratory analysis and partitioning of large-scale networks. SNAP is implemented in C, uses OpenMP primitives for parallelization, and targets sequential, multicore, and symmetric multiprocessor platforms. Our intent with SNAP is to provide a simple and intuitive interface for network analysis and application design, hiding the parallel programming complexity from the user. In addition to path-based, centrality, and community identification queries on large-scale graphs, we support commonly-used preprocessing kernels and quantitative measures that help understand the global network topology. The latest version of SNAP (0.4) was released in August 2010. Sponsors: This work was supported in part by NSF Grants CAREER CCF-0611589, NSF DBI-0420513, ITR EF/BIO 03-31654, IBM Faculty Fellowship and Microsoft Research grants, NASA grant NP-2005-07-375-HQ, and DARPA Contract NBCH30390004. Keywords: network, analysis, software, graph, traversal, betweenness centrality, community, identification, multicore,

Proper citation: Small-world Network Analysis and Partitioning (RRID:SCR_013662) Copy   

•   Source: SciCrunch Registry

http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula

Software tool developed for automatically reconstructing a set of major white matter pathways in the brain from diffusion weighted images using probabilistic tractography. This method utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual intervention with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user''''s preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons.

Proper citation: TRACULA (RRID:SCR_013152) Copy   

•   Source: SciCrunch Registry

http://www.omicsdi.org/

Portal for dataset discovery across a heterogeneous, distributed group of transcriptomics, genomics, proteomics and metabolomics data resources. These resources span eight repositories in three continents and six organisations, including both open and controlled access data resources.

Proper citation: Omics Discovery Index (RRID:SCR_010494) Copy   

•   Source: SciCrunch Registry

http://subread.sourceforge.net/

Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread.

Proper citation: Subread (RRID:SCR_009803) Copy   

•   Source: SciCrunch Registry

http://pa.wishartlab.com/pa/pa/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Web-based tool that predicts subcellular localization and GO molecular function of proteins. Proteome Analyst has the ability to explain its predictions and gives users the ability to run a large set of tools on their proteins.

Proper citation: Proteome Analyst (RRID:SCR_013807) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/ibdreg/index.html

Software package in S-PLUS and R to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree. (entry from Genetic Analysis Software)

Proper citation: IBDREG (RRID:SCR_013127) Copy   

•   Source: SciCrunch Registry

https://github.com/eead-csic-compbio/split_pairs

Software for processing NGS sequence reads in FASTQ and FASTA formats. split_pairs.pl is suited particularly for the task of sorting pair end reads and for modifying their headers with Perl-style regular expressions.

Proper citation: split_pairs.pl (RRID:SCR_015707) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/intact/complex/#annotations:fIzBXhJPEeej78Pl6R0ScA

Database and encyclopaedic resource of macromolecular complexes found in key model organisms from scientific literature. Data includes protein-only complexes, protein-small molecules, and protein-nucleic acid complexes. The information within the portal is manually curated and available for download.

Proper citation: Complex Portal (RRID:SCR_015038) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gsa-snp/

A tool for the gene-set (or pathway) analysis of a genome-wide association study result. It accepts a genome-wide list of SNPs and their association P-values. It summarizes the SNP P-values into nearby genes. The gene-by-gene summary results are then further summarized by gene-sets such as Gene Ontology, KEGG pathways, or user-created gene-sets. Various standardization and statistical tests can be performed and the resulting gene-sets that pass a significance level after multiple-testing correction are reported. The tool is written in Java and is available as a standalone version.

Proper citation: GSA-SNP (RRID:SCR_013109) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data.

Proper citation: Trim Galore (RRID:SCR_011847) Copy   

•   Source: SciCrunch Registry

http://www.aiddata.org/

Portal of information about international economic development assistance, dating back to 1947, that includes a database of nearly one million past and present aid activities around the world, aid information management services and tools, data visualization technologies, and research designed to increase understanding of development finance. AidData is searchable by topic such as disaster prevention, energy supply, water supply or reconstruction relief. You may also search by specific regions including Africa, Europe, America, Asia, or Oceania.

Proper citation: AidData (RRID:SCR_010480) Copy   

•   Source: SciCrunch Registry

http://www.aoos.org/

Portal for ocean and coastal observations data. They address regional and national needs for ocean information, gather specific data on key coastal and ocean variables, and ensure timely and sustained dissemination and availability of these data. . AOOS programmatic focus areas are: * Safe marine operations * Coastal hazard mitigation * Tracking ecosystem and climate trends * Monitoring water quality

Proper citation: Alaska Ocean Observing System (RRID:SCR_010481) Copy   

•   Source: SciCrunch Registry

http://ncmir.ucsd.edu/Software/btrack.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. It analyzes and graphs time-lapse imaging data as acquired by a Bio-Rad confocal microscope, for experiments using nonratiometric fluorescent indicator dyes. Btrack can accommodate changes in the positions of imaged cells/tissue regions and can be used for analyzing an unlimited number of areas (cells/tissue regions) in an imaged field.

Proper citation: btrack (RRID:SCR_013591) Copy   

•   Source: SciCrunch Registry

http://dels.nas.edu/ilar

The mission of ILAR is to evaluate and disseminate information on issues related to the scientific, technological, and ethical use of animals and related biological resources in research, testing, and education. Using the principles of refinement, reduction, and replacement (3Rs) as a foundation, ILAR promotes high-quality science through the humane care and use of animals and the implementation of alternatives. Through the reports of expert committees, the ILAR Journal, web-based resources, and other means of communication, ILAR functions as a component of the National Academies to provide independent, objective advice to the federal government, the international biomedical research community, and the public. ILAR supports the responsible use of animals in research, testing, and education as a key component to advancing the health and quality of life of humans and animals. It promotes high-quality science and humane care and use of research animals based upon the principles of refinement, replacement, and reduction (the 3Rs) and high ethical standards. It fosters best practices that enhance human and animal welfare by organizing and disseminating information and by facilitating dialogue among interested parties. It has developed a unique Search Engine to search for animal models and strains. This search engine surveys all the websites of vendors and repositories of laboratory animals and biological material on our Links page. The ILAR develops guidelines on laboratory animal care and use and conducts conferences, symposia, and workshops on important laboratory animal problems. ILAR publishes the ILAR Journal on a quarterly basis, as well as conference proceedings and special reports prepared by committees of experts. A list of ILAR publications on issues related to laboratory animal research is available on the Web site. As part of the Animal Models and Genetic Stocks Information Exchange Program, ILAR staff members answer direct telephone and mail inquiries and maintain a Web page containing a database on animal models and genetic stock. The Web site also offers a comprehensive search engine that enables users to find information on the existence and location of special animal models, correct nomenclature to identify animals, and related topics such as diseases of animals and relevant publications. Sponsors: ILAR receives funding from the following sponsors: -Abbott Laboratories -Abbott Fund -American College of Laboratory Animal Medicine (ACLAM) -American Society of Laboratory Animal Practitioners (ASLAP) -Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) -Bristol-Myers Squibb Co. -Charles River -Charles River Laboratories Foundation -Covance -Federation of American Societies for Experimental Biology (FASEB) -GlaxoSmithKline -Merck & Co., Inc. -National Science Foundation (NSF) -Pfizer -Scientists Center for Animal Welfare (SCAW) -U.S. Department of Agriculture (USDA) -U.S. Department of the Army -U.S. Department of Health and Human Services (DHHS) :*National Institutes of Health (NIH) :*Office of Research Integrity (ORI) -U.S. Department of the Navy -U.S. Department of Veterans Affairs -Wellcome Trust -Wyeth Pharmaceuticals

Proper citation: Institute for Laboratory Animal Research (RRID:SCR_006872) Copy   

•   Source: SciCrunch Registry

https://www.amazon.com/How-Brain-Works-Mark-Dubin/dp/0632044411

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Is the Brain (Like) a Computer is an e-book written by Prof. Mark Dubin. It consists of the following: Introduction. Why do we consider the relationship of brains and computers and what does this have to do with consciousness? What's a Brain Made Of? A thought experiment. Test Drive a Turing Machine. A theoretical approach. Interim Summary. Many of the main pages have links to additional information. When you click on one of those links a NEW page will open ON TOP of the page you are clicking from. This convention is adopted so that you can look at the additional information and then easily return to the main page you got there from.

Proper citation: Is the Brain (Like) a Computer (RRID:SCR_008809) Copy   

•   Source: SciCrunch Registry

https://web.njit.edu/~matveev/calc.html

A modeling tool for simulating intracellular calcium diffusion and buffering. CalC solves continuous reaction-diffusion PDEs describing the entry of calcium into a volume through point-like channels, and its diffusion, buffering and binding to calcium receptors. Its features include: being platform-independent; being operated by simple script; combinable with MATLAB; and providing real-time views. Demos and manuals are provided on the website.

Proper citation: CalC (RRID:SCR_014259) Copy   

•   Source: SciCrunch Registry