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https://code.google.com/p/gel2de/

Software application for performing pixel-by-pixel correlation analysis on a set of gel images from two-dimensional gel electrophoresis and a set of clinical parameters for a population. The application is written in C++, and has been tested on Windows, although it in principle should compile cross platform using CMake.

Proper citation: Gel2DE (RRID:SCR_002977) Copy   

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http://www.wellesley.edu/Neuroscience/

Neuroscience was implemented as a new interdisciplinary major in 1999, replacing the Psychobiology Program and providing a base of experiences in biology, chemistry and psychology. Our students benefit from being able to work in small classes and to experience investigative lab experiences even in their introductory courses. Wellesley's neuroscience majors graduate with a liberal arts background coupled with sufficient concentration in this specialized field to be competitive among students coming from exclusively research-oriented institutions. The best proofs of the success of this approach are its products: * 60% of our graduates proceed to medical school; * 15% of our graduates continue on with graduate work in neuroscience, psychology, or neuropsychology; * 10% of our graduates pursue careers that intersect with neuroscience - for example, patent law or work in the biotech industry. Neuroscience is the study of the structure and function of neurons and how they are assembled to produce behaviors. This topic uses a multidisciplinary approach that extends from the molecular, through the cellular, and to the behavioral level.

Proper citation: Wellesley College Neuroscience (RRID:SCR_002734) Copy   

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http://selectscience.net

SelectScience.net is a leading online resource for applied chemists, clinical chemists and life scientists. It provides up-to-date product and industry news, an extensive product directory and end-user product reviews, as well as the ability for visitors to review the products they use. Scientists can also use the site to search for jobs, application notes and scientific conferences. Sponsors: The company is run by independent scientists and funded from Government and Corporate sponsorship.

Proper citation: SelectScience (RRID:SCR_002733) Copy   

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

Software tool to visualize and analyse ChIP-on-chip array data. Main features: * Import of data from Nimblegen arrays (other formats can be added if people send us examples) * Normalization of data (both per array and per probe) * Various data plotting options to assess data quality and the effectiveness of normalization * Creation of data groups for visualization and analysis * Visualization of data against an annotated genome. * Statistical analysis of data to find probes of interest * Creation of reports containing probes, data and genome annotation Note: This project is no longer being developed, but critical bug fixes will still be provided

Proper citation: ChIPMonk (RRID:SCR_002975) Copy   

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https://code.google.com/p/ms-lims/

Software that provides a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data.

Proper citation: ms lims (RRID:SCR_002974) Copy   

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http://bmsr.usc.edu/software/eons/

Modeling platform to study the basic interactions between synaptic elements that allows the user to study qualitatively, and also quantitatively the relative contributions of diverse mechanisms underlying synaptic efficacy: the relevance of each and every element that comprises a synapse, the interactions between these components and their subcellular distribution, as well as the influence of synaptic geometry (presynaptic terminal, cleft and postsynaptic density). This platform consists of a graphical interface in which elements that comprise a single glutamatergic synapse (both pre- and post-synaptically), their behavior as well as the underlying synaptic geometry can be modified. For example, EONS offers the ability to study the effect of voltage-gated calcium channels density and distribution, the number and location of receptors and more. EONS is a parametric model of a generic glutamatergic synapse that takes into account pre-synaptic mechanisms, such as calcium buffering and diffusion, neurotransmitter release, diffusion and uptake in the cleft, and postsynaptic elements, such as ionotropic AMPA and NMDA receptors, their distribution and synaptic geometry, as well as metabotropic glutamate receptors. There are no complicated equations to write: all the models are predefined. This version is a great tool for first time users and students interested in learning about synapses, as well as for studying geometry and distribution hypotheses in a 2D rectangular geometry. System Requirements: EONS V1.2 is a Windows program but can be also successfully installed and run on Mac and Linux.

Proper citation: EONS (RRID:SCR_002979) Copy   

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http://trans.nih.gov/bmap/resources/resources.htm

As part of BMAP gene discovery efforts, mouse brain cDNA libraries and Expressed Sequence Tags (ESTs) have been generated. Through this project a BMAP mouse brain UniGene set consisting of over 24,000 non-redundant members of unique clusters has been developed from EST sequencing of more than 50,000 cDNA clones from 10 regions of adult mouse brain, spinal cord, and retina (http://brainEST.eng.uiowa.edu/). In 2001, NIMH along with NICHD, NIDDK, and NIDA, awarded a contract to the University of Iowa ( M.B. Soares, PI) to isolate full-length cDNA clones corresponding to genes expressed in the developing mouse nervous system and determine their full-coding sequences. The BMAP mouse brain EST sequences can be accessed at NCBI's dbEST database (http://www.ncbi.nlm.nih.gov/dbEST/). Arrayed sets of BMAP mouse brain UniGenes and cDNA libraries, and individual BMAP cDNA clones can be purchased from Open Biosystems, Huntsville, AL (http://www.openbiosystems.com

Proper citation: BMAP cDNA Resources (RRID:SCR_002973) Copy   

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https://github.com/zd1/telseq

Software that measures average telomere length from whole genome or exome shotgun sequence data.

Proper citation: TelSeq (RRID:SCR_002730) Copy   

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http://www.ebi.ac.uk/imgt/hla/

Database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. It currently contains 9,310 allele sequences (2013) along with detailed information concerning the material from which the sequence was derived and data on the validation of the sequences. It is established procedure for authors to submit the sequences directly to the IMGT/HLA Database for checking and assignment of an official name prior to publication, this avoids the problems associated with renaming published sequences and the confusion of multiple names for the same sequence. The need for reasonably rapid publication of new HLA allele sequences has necessitated an annual meeting of the WHO Nomenclature Committee for Factors of the HLA System. Additionally they now publish monthly HLA nomenclature updates both in journals and online to provide quick and easy access to new sequence information. The IMGT/HLA Database is part of the international ImMunoGeneTics project. In collaboration with the Imperial Cancer Research Fund (ICRF) and European Bioinformatics Institute (EBI) they have developed an Oracle database to house the HLA sequences in such a way as to allow users to present complex queries about the sequence, sequence features, references, contacts and allele designations to the database via a graphical user interface over the web. The IMGT/HLA Database Submission Tool allows direct submission of sequences to the WHO HLA Nomenclature Committee for Factors of the HLA System. The IMGT/HLA Database provides an FTP site for the retrieval of sequences in a number of pre-formatted files.

Proper citation: IMGT/HLA (RRID:SCR_002971) Copy   

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http://www.jove.com/neuro

A peer reviewed, PubMed indexed journal devoted to the publication of biological research in a video format.

Proper citation: Journal of Visualized Experiments (RRID:SCR_002966) Copy   

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https://www.innopsys.com/en/lifesciences-products/microarrays/software

System control software used for data acquisition and analysis for microarray images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Mapix (RRID:SCR_002723) Copy   

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http://www.scienceexchange.com/facilities/igentbio

A commercial facility handling induced pluripotent stem cell (iPSC) generation, cellular characterization, teratoma formation, karyotyping, and KO-mouse generation.

Proper citation: iGentBio (RRID:SCR_002722) Copy   

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http://www.gensat.org/

Gene expression data and maps of mouse central nervous system. Gene expression atlas of developing adult central nervous system in mouse, using in situ hybridization and transgenic mouse techniques. Collection of pictorial gene expression maps of brain and spinal cord of mouse. Provides tools to catalog, map, and electrophysiologically record individual cells. Application of Cre recombinase technologies allows for cell-specific gene manipulation. Transgenic mice created by this project are available to scientific community.

Proper citation: Gene Expression Nervous System Atlas (RRID:SCR_002721) Copy   

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http://www.nest-simulator.org/

Software tool as simulator for spiking neural network models that focuses on dynamics, size and structure of neural systems rather than on exact morphology of individual neurons. Used for any size spiking neurons networks including models of information processing, models of network activity dynamics, models of learning and plasticity.

Proper citation: NEST Simulator (RRID:SCR_002963) Copy   

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http://osdoc.cogsci.nl/

Software for the rapid development of psychological and neuroscientific experiments.

Proper citation: OpenSesame (RRID:SCR_002849) Copy   

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http://www.hgsc.bcm.tmc.edu/content/red-flour-beetle-genome-project

This portal provides information about the Tribolium castabeum Genome Project. The Tribolium castaneum genome sequence and its analysis has been published in Nature, two companion journal issues (IBMB and DGE) and numerous other publications listed below. The red flour beetle, Tribolium castaneum, a common pest that is also a genetic model for the Coleoptera. The genome has been sequenced to 7-fold coverage using a whole genome shotgun approach and assembled using the HGSC's assembly engine, Atlas, with methods employed for the Drosophila pseudoobscura genome assembly. Approximately 90% of the genome sequence has been mapped to chromosomes in collaboration with Dick Beeman (USDA ARS) and Sue Brown (Kansas State University). Access to the Data :- Genome Assembly: The long term home of the Tribolium genome is Beetlebase. Tcas 3.0 is now available in GenBank and on our FTP site. Note there are no restrictions of any kind on the Tribolium data as it has been published. Version 2 of the assembly, Tcas_2.0 is available for download using the FTP Data link in the sidebar. The assembly is described in detail in the README in that directory. T.cas_1.0 was a preliminary genome assembly that did not include large insert paired end information and has been moved to a previous assemblies folder. A genboree browser of the Tcas2.0 sequence is available here: There are also links to the genboree browser from the blast results (at the bottom of each reported HSP) if you use the blast server on this page. The original linear scaffold file, Tcas2.0/linearScaffolds/Tcas20050914-genome, posted on the ftp site did not include singleton contigs from the assembly and thus did not fully reflect the tribolium genome sequence, missing ~4.4Mb of sequence in 1860 contigs and reptigs or approximately 2.5% of the assembled sequence. A corrected Tcas20051011-genome file containing these missing sequences is now available on the ftp site. The blast databases have also been updated to reflect this change. All other data is correct, and not affected by this change. :- BLAST Searches: The BLAST link is located in the sidebar. :* Linearized chromosome and unplaced scaffold sequences :* Assembled contigs :* Bin0 unassembled reads and Repeat reads Traces are available from the NCBI Trace Archive by using the link in the sidebar, or by using NCBI MegaBLAST with a same species or cross species query. Sponsors: Funding for this project has been provided by the National Human Genome Research Institute (NHGRI U54 HG003273), which is part of the National Institutes of Health (NIH), and the U.S. Department of Agriculture's Agricultural Research Service (USDA ARS Agreement No. 58-5430-3-338).

Proper citation: Tribolium castaneum Genome Project (RRID:SCR_002848) Copy   

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http://swift.cmbi.ru.nl/gv/dssp/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB) and the program that calculates DSSP entries from PDB entries. DSSP is distributed on a basis of trust and instructions are available on the site. * Precompiled executables are also available for Linux and Windows. (The Windows .exe file was compiled under Linux using Mingw32, has never seen a Windows environment and should thus be virus-free. Download the source if you want to be 100% sure.) Under Windows the DSSP output does not make it to the console, so redirect it to a file instead: dsspcmbi source.pdb destination.dssp > messages.txt * Several changes have been made to the DSSP program to solve problems with recent PDB files. These are documented in the source code. * FTP access to the DSSP files resides at the CMBI: ftp.cmbi.kun.nl/pub/molbio/data/dssp or ftp://ftp.ebi.ac.uk/pub/databases/dssp/. If you have problems downloading the DSSP files, it is likely that your FTP program is not able to handle tens of thousands of files in one directory. In this case, install a proper FTP program, for example NCFTP. However, it is recommended that you download DSSP files with the rsync command.

Proper citation: Database of Secondary Structure Assignments (RRID:SCR_002725) Copy   

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http://hapmap.ncbi.nlm.nih.gov/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project.

Proper citation: International HapMap Project (RRID:SCR_002846) Copy   

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http://hembase.niddk.nih.gov/

Database designed for web-based examination of the human erythroid transcriptome. The database is organized to provide a cytogenetic band position, a unique name as well as a concise annotation for each entry. Search queries may be performed by name, keyword or cytogenetic location. Search results are linked to primary sequence data and three major human genome browsers for access to information considered current at the time of each search. Hembase provides interested scientists and clinical hematologists with a genome-based approach toward the study of erythroid biology. Red blood cells in the circulation arise from hematopoietic stem cells that proliferate as erythroid progenitors and differentiate into erythroid precursor cells in response to the hormone erythropoietin. Messenger RNA was isolated from those cells and used to generate gene libraries. Sequencing several thousand expressed sequence tags (EST) from those libraries was then performed. Those EST and sequences encoding several hundred additional genes with known expression in erythroid cells are compiled here as a database of human erythroid gene activity. The database is organized and linked according to the location of these sequences within the human genome., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: HemBase (RRID:SCR_002880) Copy   

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http://www.pathway.com/

The mission of Pathway Genomics is to empower you with the most secure, comprehensive and affordable personal genomic information available and to become your partner in utilizing that information to improve your health and wellness. Pathway is the only DNA testing service with an on-site federal and state CLIA-licensed laboratory. This means it offers: - Better Science: Its certified geneticists are on-staff and on-site in our own state-of-the-art laboratory in California. Their 10,600 square foot, high-complexity CLIA licensed lab facility is equipped with the latest high-throughput robotics and Affymetrix, Illumina and Sequenom genotyping equipment. As scientists committed to staying on the cutting-edge, they diligently monitor all new developments in the rapidly evolving DNA research field allowing us to provide you immediate access to more meaningful markers than any other DNA testing firm. - Better Security: Because Pathway Genomics has its own laboratory, your DNA never leaves the building, and is never shared with third parties. At Pathway Genomics the integrity of your genetic material and information are protected. Instead, enjoy the security of our proprietary DNA Lockbox. Everyone has the right to know the secrets hidden within their own DNA. That's why Pathway has created the most secure, comprehensive and affordable way to unlock those secrets. This way you can: - Identify genetic health and drug response - Personalize your medical care - Help your doctor help you - Uncover your ancestral path - Explore the traits that make you unique With Personal DNA Testing, you can take preventative steps to improve your future, and even extend your life. Pathway Genomics provides cutting-edge research and easy-to-read scientific information customized for you, and you alone, based on your genes and your lifestyle. For the first time in human history, modern science has made it possible for you to learn your genetic predisposition for more than 90 diseases and conditions, drug responses and pre-pregnancy carrier status. With this powerful knowledge and our easy-to-understand guidance, you can modify your health regime so that you may live a healthier, longer life. DNA testing will discover more about your personal heritage than you ever thought possible. We uncover your deep ancestry by taking giant leaps into the past, going back more than 10,000 years. We test both your mitochondrial DNA, which is passed down from mother to child and reveals your direct maternal ancestry; and your Y chromosome (males only), which is passed down from father to son and reveals your direct paternal ancestry. If you're like most people, you've always wondered about the genes you have inherited and what traits you will pass on to future generations. Discover your genetically inherited predispositions and characteristics and whether they are beneficial or potentially harmful. You may also find that some traits are simply fun to uncover.

Proper citation: Pathway Genomics (RRID:SCR_002883) Copy   

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