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http://www.neuroconstruct.org/

Software for simulating complex networks of biologically realistic neurons, i.e. models incorporating dendritic morphologies and realistic cell membrane conductance, implemented in Java and generates script files for the NEURON and GENESIS simulators, with support for other simulation platforms (including PSICS and PyNN) in development. neuroConstruct is being developed in the Silver Lab in the Department of Neuroscience, Physiology and Pharmacology at UCL and uses the latest NeuroML specifications, including MorphML, ChannelML and NetworkML. Some of the key features of neuroConstruct are: Creation of networks of biologically realistic neurons, positioned in 3D space. Complex connectivity patterns between cell groups can be specified for the networks. Can import morphology files in GENESIS, NEURON, Neurolucida, SWC and MorphML format for inclusion in network models. Simulations can be run on the NEURON or GENESIS platforms. Cellular processes (synapses/channel mechanisms) can be imported from native script files or created in ChannelML. Recording of simulation data generated by the simulation and visualization/analysis of data. Stored simulation runs can be viewed and managed through the Simulation Browser interface.

Proper citation: neuroConstruct (RRID:SCR_007197) Copy   

•   Source: SciCrunch Registry

https://bams1.org/

Knowledge management system designed to handle neurobiological information at different levels of organization of vertebrate nervous system. Database and repository for information about neural circuitry, storing and analyzing data concerned with nomenclature, taxonomy, axonal connections, and neuronal cell types. Handles data and metadata collated from original literature, or inserted by scientists that is associated to four levels of organization of vertebrate nervous system. Data about expressed molecules, neuron types and classes, brain regions, and networks of brain regions.

Proper citation: Brain Architecture Management System (RRID:SCR_007251) Copy   

•   Source: SciCrunch Registry

http://human.brain-map.org/static/brainexplorer

Multi modal atlas of human brain that integrates anatomic and genomic information, coupled with suite of visualization and mining tools to create open public resource for brain researchers and other scientists. Data include magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), histology and gene expression data derived from both microarray and in situ hybridization (ISH) approaches. Brain Explorer 2 is desktop software application for viewing human brain anatomy and gene expression data in 3D.

Proper citation: Allen Human Brain Atlas (RRID:SCR_007416) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/genbank/dbest/

Database as a division of GenBank that contains sequence data and other information on single-pass cDNA sequences, or Expressed Sequence Tags, from a number of organisms.

Proper citation: dbEST (RRID:SCR_008132) Copy   

•   Source: SciCrunch Registry

http://wwwmgs.bionet.nsc.ru/mgs/gnw/about.shtml

GeneNetWorks is designed for accumulation of experimental data, data navigation, data analysis, and analysis of dependencies in the field of gene expression regulation. It integrates the databases and programs for processing the data about structure and function of DNA, RNA, and proteins, together with the other information resources important for gene expression description. The unique property of above described system is that all the resources within the system GeneNetWorks are divided according to the natural hierarchy of molecular genetic systems and has the following levels: (1) DNA; (2) RNA; (3) proteins; and (4) gene networks. Each module contains: 1) experimental data represented as a database or some sample; 2) program for data analysis; 3) results of an automated data processing; 4) tools for the graphical representation of these data and the results of the data analyses.

Proper citation: GeneNetWorks (RRID:SCR_008034) Copy   

•   Source: SciCrunch Registry

http://www.genomatix.de/

Genomatix is a privately held company that offers software, databases, and services aimed at understanding gene regulation at the molecular level representing a central part of systems biology. Its multilayer integrative approach is a working implementation of systems biology principles. Genomatix combines sequence analysis, functional promoter analysis, proprietary genome annotation, promoter sequence databases, comparative genomics, scientific literature data mining, pathway databases, biological network databases, pathway analysis, network analysis, and expression profiling into working solutions and pipelines. It also enables better understanding of biological mechanisms under different conditions and stimuli in the biological context of your data. Some of Genomatix'' most valuable assets are the strong scientific background and the years of experience in research & discovery as well as in development & application of scientific software. Their firsthand knowledge of all the complexities involved in the in-silico analysis of biological data makes them a first-rate partner for all scientific projects involving the evaluation of gene regulatory mechanisms. The Genomatix team has more than a decade of scientific expertise in the successful application of computer aided analysis of gene regulatory networks, which is reflected by more than 150 peer reviewed scientific publications from Genomatix'' scientists More than 35,000 researchers in industry and academia around the world use this technology. The software available in Genomatix are: - GenomatixSuite: GenomatixSuite is our comprehensive software bundle including ElDorado, Gene2Promoter, GEMS Launcher, MatInspector and MatBase. GenomatixSuite PE also includes BiblioSphere Pathway Edition. Chromatin IP Software - RegionMiner: Fast, extensive analysis of genomic regions. - ChipInspector: Discover the real power of your microarray data. Genome Annotation Software - ElDorado: Extended Genome Annotation. - Gene2Promoter: Retrieve & analyze promoters - GPD: The Genomatix Promoter Database, which is now included with Gene2Promoter. Knowledge Mining Software - BiblioSpere : The next level of pathway/genomics analysis. - LitInspector: Literature and pathway analysis for free. Sequence Analysis Software - GEMS Launcher: Our integrated collection of sequence analysis tools. - MalInspector: Search transcription factor binding sites - MatBase: The transcription factor knowledge base. Other (no registration required) Software - DiAlign: Multiple alignment of DNA/protein sequence. - Genomatix tools: Various small tools for sequence statistics, extraction, formatting, etc.

Proper citation: Genomatix Software: Understanding Gene Regulation (RRID:SCR_008036) Copy   

•   Source: SciCrunch Registry

http://www.biodas.org

The Distributed Annotation System (DAS) defines a communication protocol used to exchange annotations on genomic or protein sequences. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients. The advantages of this system are that control over the data is retained by data providers, data is freed from the constraints of specific organisations and the normal issues of release cycles, API updates and data duplication are avoided. DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up sequence annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities. A DAS-enabled website or application can aggregate complex and high-volume data from external providers in an efficient manner. For the biologist, this means the ability to plug in the latest data, possibly including a user''s own data. For the application developer, this means protection from data format changes and the ability to add new data with minimal development cost. Here are some examples of DAS-enabled applications or websites for end users: :- Dalliance Experimental Web/Javascript based Genome Viewer :- IGV Integrative Genome Viewer java based browser for many genomes :- Ensembl uses DAS to pull in genomic, gene and protein annotations. It also provides data via DAS. :- Gbrowse is a generic genome browser, and is both a consumer and provider of DAS. :- IGB is a desktop application for viewing genomic data. :- SPICE is an application for projecting protein annotations onto 3D structures. :- Dasty2 is a web-based viewer for protein annotations :- Jalview is a multiple alignment editor. :- PeppeR is a graphical viewer for 3D electron microscopy data. :- DASMI is an integration portal for protein interaction data. :- DASher is a Java-based viewer for protein annotations. :- EpiC presents structure-function summaries for antibody design. :- STRAP is a STRucture-based sequence Alignment Program. Hundreds of DAS servers are currently running worldwide, including those provided by the European Bioinformatics Institute, Ensembl, the Sanger Institute, UCSC, WormBase, FlyBase, TIGR, and UniProt. For a listing of all available DAS sources please visit the DasRegistry. Sponsors: The initial ideas for DAS were developed in conversations with LaDeana Hillier of the Washington University Genome Sequencing Center.

Proper citation: Distributed Annotation System (RRID:SCR_008427) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/nitrc_es/

Support and community integration for the enhanced NITRC services of the Image Repository (IR) and the Computational Environment (CE). The NITRC Computational Environment, an on-demand, cloud based computational virtual machine pre-installed with popular NITRC neuroimaging tools built using NeuroDebian. NITRC Image Repository is built upon XNAT and supports both NIfTI and DICOM images. The NITRC-IR offers 3,733 Subjects, and 3,743 Imaging Sessions searchable across seven projects to promote re-use and integration of valuable NIH-funded data.

Proper citation: NITRC Enhanced Services (RRID:SCR_002494) Copy   

•   Source: SciCrunch Registry

http://www.fmrib.ox.ac.uk/fsl/

Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas.

Proper citation: FSL (RRID:SCR_002823) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/

Community portal for researchers and content management system for data and databases. Intended to provide common source of data to research community and data about Research Resource Identifiers (RRIDs), which can be used in scientific publications. Central service where RRIDs can be searched and created. Designed to help communities of researchers create their own portals to provide access to resources, databases and tools of relevance to their research areas. Adds value to existing scientific resources by increasing their discoverability, accessibility, visibility, utility and interoperability, regardless of their current design or capabilities and without need for extensive redesign of their components or information models. Resources can be searched and discovered at multiple levels of integration, from superficial discovery based on limited description of resource at SciCrunch Registry, to deep content query at SciCrunch Data Federation.

Proper citation: SciCrunch (RRID:SCR_003115) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/arrayexpress/

International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus.

Proper citation: ArrayExpress (RRID:SCR_002964) Copy   

•   Source: SciCrunch Registry

http://developingmouse.brain-map.org/

Map of gene expression in developing mouse brain revealing gene expression patterns from embryonic through postnatal stages. Provides information about spatial and temporal regulation of gene expression with database. Feature include seven sagittal reference atlases created with a developmental ontology. These anatomic atlases may be viewed alongside in situ hybridization (ISH) data as well as by itself.

Proper citation: Allen Developing Mouse Brain Atlas (RRID:SCR_002990) Copy   

•   Source: SciCrunch Registry

http://childes.talkbank.org/

Child language component of TalkBank system. TalkBank is system for sharing and studying conversational interactions. Includes software developed for speech recognition and analysis as well as behavior recognition. Database contains transcript and media data collected from conversations between young children and their playmates and caretakers. Conversations with older children and adults are available from TalkBank. All of data is transcribed in CHAT and CA/CHAT formats.

Proper citation: Child Language Data Exchange System (CHILDES) (RRID:SCR_003241) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/jmosaics.html

R software that detects enriched regions of ChIP-seq data sets jointly.

Proper citation: Jmosaics (RRID:SCR_001094) Copy   

•   Source: SciCrunch Registry

http://www.farsight-toolkit.org/wiki/FARSIGHT_Toolkit

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A collection of software modules for image data handling, pre-processing, segmentation, inspection, editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks. All of the modules are written in accordance with software practices of the Insight Toolkit Community. Importantly, all modules are accessible through the Python scripting language which allows users to create scripts to accomplish sophisticated associative image analysis tasks over multi-dimensional microscopy image data. This language works on most computing platforms, providing a high degree of platform independence. Another important design principle is the use of standardized XML file formats for data interchange between modules.

Proper citation: Farsight Toolkit (RRID:SCR_001728) Copy   

•   Source: SciCrunch Registry

http://incf.org/programs/atlasing/projects/waxholm-space

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 1st, 2023. Coordinate based reference space for the mapping and registration of neuroanatomical data. Users can download image volumes representing the canonical Waxholm Space (WHS) adult C57BL/6J mouse brain, which include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel University), and a volume of labels. All volumes are represented at 21.5μ isotropic resolution. Datasets are provided as gzipped NIFTI files.

Proper citation: Waxholm Space (RRID:SCR_001592) Copy   

•   Source: SciCrunch Registry

http://www.ncibi.org/

The Center develops conceptual models, computational infrastructure, an integrated knowledge repository, and query and analysis tools that enable scientists to effectively access and integrate the wealth of biological data. The National Center for Integrative Biomedical Informatics (NCIBI) was founded in October 2005 and is one of seven National Centers for Biomedical Computing (NCBC) in the NIH Roadmap. NCIBI is based at the University of Michigan as a part of the Center for Computational Medicine and Biology (CCMB). NCIBI is composed of biomedical researchers, computational biologists, computer scientists, developers and human-computer interaction specialists organized into seven major core functions. They work in interdisciplinary teams to collectively develop tools that are not only computationally powerful but also biologically relevant and meaningful. The four initial Driving Biological Projects (prostate cancer progression, Type 1 and type 2 diabetes and bipolar disorder) provide the nucleation point from which tool development is informed, launched, and tested. In addition to testing tools for function, a separate team is dedicated to testing usability and user interaction that is a unique feature of this Center. Once tools are developed and validated the goal of the Center is to share and disseminate data and software throughout the research community both internally and externally. This is achieved through various mechanisms such as training videos, tutorials, and demonstrations and presentations at national and international scientific conferences. NCIBI is supported by NIH Grant # U54-DA021519.

Proper citation: National Center for Integrative Biomedical Informatics (RRID:SCR_001538) Copy   

•   Source: SciCrunch Registry

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

Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS.

Proper citation: FreeSurfer (RRID:SCR_001847) Copy   

•   Source: SciCrunch Registry

https://dataverse.org/

Project portal for publishing, citing, sharing and discovering research data. Software, protocols, and community connections for creating research data repositories that automate professional archival practices, guarantee long term preservation, and enable researchers to share, retain control of, and receive web visibility and formal academic citations for their data contributions. Researchers, data authors, publishers, data distributors, and affiliated institutions all receive appropriate credit. Hosts multiple dataverses. Each dataverse contains studies or collections of studies, and each study contains cataloging information that describes the data plus the actual data files and complementary files. Data related to social sciences, health, medicine, humanities or other sciences with an emphasis in human behavior are uploaded to the IQSS Dataverse Network (Harvard). You can create your own dataverse for free and start adding studies for your data files and complementary material (documents, software, etc). You may install your own Dataverse Network for your University or organization.

Proper citation: Dataverse Network Project (RRID:SCR_001997) Copy   

•   Source: SciCrunch Registry

http://amigo.geneontology.org/

Web tool to search, sort, analyze, visualize and download data of interest. Along with providing details of the ontologies, gene products and annotations, features a BLAST search, Term Enrichment and GO Slimmer tools, the GO Online SQL Environment and a user help guide.Used at the Gene Ontology (GO) website to access the data provided by the GO Consortium. Developed and maintained by the GO Consortium.

Proper citation: AmiGO (RRID:SCR_002143) Copy   

•   Source: SciCrunch Registry