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https://github.com/UCSFBiomagneticImagingLab/nutmeg

Software MEG/EEG analysis toolbox for reconstructing neural activation and overlaying it onto structural MR images. Toolbox runs under MATLAB in conjunction with SPM2 and can be used with Linux/UNIX, Mac OS X, and Windows platforms.

Proper citation: NUTMEG (RRID:SCR_002748) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/gsea/

Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.

Proper citation: Gene Set Enrichment Analysis (RRID:SCR_003199) Copy   

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http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview

A Java based software tool designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable. (entry from Genetic Analysis Software) * LD & haplotype block analysis * haplotype population frequency estimation * single SNP and haplotype association tests * permutation testing for association significance * implementation of Paul de Bakker's Tagger tag SNP selection algorithm. * automatic download of phased genotype data from HapMap * visualization and plotting of PLINK whole genome association results including advanced filtering options Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. Note: Haploview is currently on a development and support freeze. The team is currently looking at a variety of options in order to provide support for the software. Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site.

Proper citation: Haploview (RRID:SCR_003076) Copy   

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http://www.brainscape.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 23, 2013. Database for resting state functional connectivity studies. Functional connectivity has shown tremendous promise in mapping the intrinsic functional topography of the brain, evaluating neuroanatomical models, and investigating neurological and psychiatric disease. Brainscape includes a repository of public and private data and an analysis engine for exploring the correlation structure of spontaneous fluctuations in the fMRI BOLD signal. (DICOM data is the image format that can be uploaded.) With Brainscape you can upload, analyze, and share your own data. You can search for, download, and analyze studies in the repository of shared data. The analysis engine works by selecting one or more studies, typing in the coordinates of a brain region of interest, and the seed-region correlation engine computes the correlation structure across the whole brain. (T1, T2 and EPI data are the scan types Brainscape can process.) You decide who can access your data. You can keep it to yourself, share with select colleagues, or share it with everyone. The Brainscape database and analysis tools are open source and freely available.

Proper citation: Brainscape (RRID:SCR_002962) Copy   

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http://www.mrc-cbu.cam.ac.uk/Imaging

Portal where neuroimaging studies are carried out using a Siemens 3T Tim Trio Magnetic Resonance Imaging (or MRI) scanner that is wholly dedicated to studies in Cognitive Neuroscience. From emotions and memories to language and learning, functional neuroimaging is being applied in many different areas of Cognitive Neuroscience. In many cases, this research relies upon support from healthy volunteers although neuroimaging studies are also being conducted in various clinical populations, including depression, anxiety, Parkinson's disease and Alzheimer's disease.

Proper citation: CBU Imaging Wiki (RRID:SCR_003014) Copy   

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http://iimcb.genesilico.pl/MetaLocGramN/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A tool for subcellular localization prediction of Gram-negative proteins. You can also use MetaGramLocN via SOAP. SOAP enables you to invoke our method from scripts written in your programming language of choice.

Proper citation: MetaLocGramN (RRID:SCR_003154) Copy   

•   Source: SciCrunch Registry

http://cytoscape.org

Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

Proper citation: Cytoscape (RRID:SCR_003032) Copy   

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http://www.plexon.com/products/map-software

A suite of client / server programs that control spike sorting in the Multichannel Acquisition Processor (MAP) Data Acquisition System (MAP System) and provides real-time data visualization and analysis. Plexon's original program supporting multichannel data acquisition is a suite of programs referred to as the Real-Time Acquisition System Programs for Unit Timing in Neuroscience software (RASPUTIN). This combination of software and hardware enables users to view waveforms, acquire action potential waveforms around a voltage-threshold crossing, sort them in real time according to their shape, record continuous analog signals, such as field potentials, eye position, blood pressure, as well as capture external digital-event data, such as individual TTL lines or multi-bit strobed word data. RASPUTIN utilizes a client/server architecture on a Microsoft Windows operating system. The server program runs the MAP box and distributes the data among a set of cooperating client programs. The program can record analog signals and spike and digital-event data in a single data file, and supports 16, 32, 48, 64, 96 and 128 channel configurations. RASPUTIN's operation is based on two primary programs: Sort Client and MAP Server. The Sort Client is the primary control program for the MAP System hardware and may be used to adjust the MAP operating parameters (e.g., amplification, filtering) and to set the specific sorting parameters for each channel. MAP Server is the low-level interface for configuring the MAP, which transfers commands such as gain and filter changes or parameter settings from the various clients to the MAP box. MAP Server also accumulates data coming from the MAP box in a circular buffer memory. The client programs connect to MAP Server to gain access to that data. MAP Server also mediates communication between the clients, keeping them informed of commands sent to the MAP from other clients. RASPUTIN is not sold separately, but rather arrives pre-loaded on the MAP Control Computer with the purchase of any MAP System. As the MAP System has been replaced by the advanced OmniPlex D Neural Data Acquisition System, Plexon is no longer developing the RASPUTIN software program.

Proper citation: MAP Software (RRID:SCR_003170) Copy   

•   Source: SciCrunch Registry

https://bioimagesuiteweb.github.io/webapp/index.html

Web applications for analysis of multimodal/multispecies neuroimaging data. Image analysis software package. Has facilities for DTI and fMRI processing. Capabilities for both neuro/cardiac and abdominal image analysis and visualization. Many packages are extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. Can be intergrated with other biomedical image processing software, such as FSL, AFNI, and SPM.

Proper citation: BioImage Suite (RRID:SCR_002986) Copy   

•   Source: SciCrunch Registry

http://www.bioperl.org

BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: BioPerl (RRID:SCR_002989) Copy   

•   Source: SciCrunch Registry

http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/

Software R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Weighted Gene Co-expression Network Analysis (RRID:SCR_003302) Copy   

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http://socialbrain.wordpress.com/2009/09/30/neurovia-download-neuro-imaging-tools-software-brain-project-matlab-program-package-for-the-analysis-of-functional-neuroimages/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. These distribution sets contain software modules and/or data sets extracted from the Visualization and Analysis Software Tools (VAST) library developed at the Minneapolis VA Medical Center, the University of Minnesota and/or the International Consortium for Neuroimaging (INC) (partially funded by the Human Brain Project )

Proper citation: Software Distribution Sets (RRID:SCR_003465) Copy   

•   Source: SciCrunch Registry

http://www.scripps.edu/researchservices/dna_array/pages/Data_Analysis_GCOS.htm

Affymetrix has recently released a new software for the acquisition, management, and analysis of gene expression data. The new GeneChip Operating Software (GCOS) platform enables researchers to perform gene expression, SNP mapping and resequencing analysis with integrated data management and scalable client server configurations. * Compatible with additional Affymetrix analysis software such as Data Mining Tool (DMT) and GeneChip DNA Analysis Software (GDAS) * Supports Gene Expression, Resequencing and Genotyping Applications * Baseline Comparison Analysis Input: Affymetrix .DAT file Output: Affymetrix files (.CEL, .CHP, .RPT, .EXP, .TXT) Availability: The Core Facility has a copy of GCOS, as well as an older version of the Affymetrix software, Microarray Suite (MAS), available for use upon request.

Proper citation: GeneChip Operating Software (RRID:SCR_003408) Copy   

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http://romi.bu.edu/elisa/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. ELISA is an online database that combines functional annotation with structure and sequence homology modeling to place proteins into sequence-structure-function neighborhoods. The atomic unit of the database is a set of sequences and structural templates that those sequences encode. A graph that is built from the structural comparison of these templates is called PDUG (protein domain universe graph). It introduces a method of functional inference through a probabilistic calculation done on an arbitrary set of PDUG nodes. Further, all PDUG structures are mapped onto all fully sequenced proteomes allowing an easy interface for evolutionary analysis and research into comparative proteomics. ELISA is the first database with applicability to evolutionary structural genomics explicitly in mind.

Proper citation: Evolutionary Lineage Inferred from Structural Analysis (RRID:SCR_002343) Copy   

•   Source: SciCrunch Registry

http://sonorus.princeton.edu/hefalmp/

HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool.

Proper citation: Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome (RRID:SCR_003506) Copy   

•   Source: SciCrunch Registry

https://covic.lji.org/databases/

Serves as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them. Most potent antibodies will guide development of vaccines to stop current outbreak and protect against future pandemics.

Proper citation: CoVIC-DB Database (RRID:SCR_018339) Copy   

•   Source: SciCrunch Registry

http://www.softberry.com/

Developer of software tools for genomic research focused on computational methods of high throughput biomedical data analysis, including software to support next generation sequencing technologies, transcriptome analysis with RNASeq data, SNP detection and selection of disease specific SNP subsets. Provides custom genome annotation services.

Proper citation: SoftBerry (RRID:SCR_000902) Copy   

•   Source: SciCrunch Registry

http://www.egi.com/clinical-division/clinical-division-geodesic-eeg-components/clinical-division-net-station

APIs for Net Station data files. APIs are available for C++, C#, and Java.

Proper citation: Net Station API (RRID:SCR_000867) Copy   

•   Source: SciCrunch Registry

https://sbpdiscovery.org/research/centers/conrad-prebys-center-for-chemical-genomics/

The Conrad Prebys Center for Chemical Genomics (CPCCG) uses advanced screening technologies to identify high level chemical probes that interact with proteins involved in cellular processes. Optimization of these probes using medicinal chemistry and informatics will form the basis of a new generation of medicines. CPCCG is 1 of 4 Comprehensive Centers chosen nationally to be a part of the Molecular Libraries Probe Program (MLP), which established the Molecular Libraries Probe Production Centers Network (MLPCN). The goal is to produce small molecule probes that allow research into health and disease on the cellular level. CPCCG core services span a range of biochemical and cell-based screens for obtaining hits and provide chemistry resources for optimizing hits into probes or drug development. - Full scale screening capabilities and technology which can provide rapid screening on a broad diversity of assays and detection platforms - Several fully-integrated industrial-scale high-throughput screening (HTS) workstations - HTS microscopy/HCS and novel algorithm development for image analysis - Full hit-to-probe chemistry and exploratory pharmacology - Powerful NMR based Chemical Fragment Screening - Highly integrated informatics infrastructure and efficient data mining capabilities - Protein production facility - Cell production facility for scale-up tissue culture The CPCCG Screening Core can screen 96, 384 or 1536 well formats using either biochemical or cell-based assays, and can process over 300,000 wells per day. Total throughput capacity will climb to over 2 million compounds per day following the opening of Burnhams east coast campus in Lake Nona, Florida.

Proper citation: Conrad Prebys Center for Chemical Genomics (RRID:SCR_001687) Copy   

•   Source: SciCrunch Registry

http://www.enfin.org/

ENFIN is a virtual institute to enable systems-level integration of experimental results. It is committed to provide a Europe-wide integration of computational approaches in systems biology. Its objectives are: - To develop a shared approach between traditionally dry and traditionally wet researchers in the area of systems-level interpretation of experimental results - To develop a distributed computational platform this integration and analysis of experimental data - To directly prove that such an approach has scientific value - To encourage and participate in the critical assessment of systems-level approaches - To disseminate knowledge and techniques to other academic researchers worldwide - To disseminate knowledge and techniques to commercial researchers, in particular European SMEs - To train young European researchers from a variety of backgrounds in system-level informatics techniques. The ENFIN Network runs four major platforms: A Joint Research Program covering the fields of Discrete Function Prediction, Network Reconstruction, Systems-Level Modeling, a Provision of Analysis Tools - EnSUITE, a Platform for Data Integration - EnCORE, and training Courses and Workshops on Systems Biology. Sponsors: The ENFIN project is funded by the European Commission within its FP6 Programme, under the thematic area Life sciences, genomics and biotechnology for health,contract number LSHG-CT-2005-518254.

Proper citation: Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology (RRID:SCR_001724) Copy   

•   Source: SciCrunch Registry