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http://www.poldracklab.org/software

The Poldrack lab has developed software tools for fMRI data analysis (links on the site), experimental design, and informatics, in collaboration with several other groups. * pubbrain.org: Developed in collaboration with the UCLA Consortium for Neuropsychiatric Phenomics, this site is an automatic meta-analytic search aid that allows for visualizing PubMed searches based on published neuroanatomic findings. * LONI Probabilistic Atlas: Developed in collaboration with the UCLA Laboratory of Neuroimaging and Center for Cognitive Phenomics, this project provides free and open access to a probabilistic atlas of cortical structures in 40 healthy individuals, including all raw data. * fmripower.org: Software developed by Jeanette Mumford in the Poldrack lab for statistical power analysis for fMRI studies. * Automated ICA-based denoising: Toolbox developed by Jussi Tohka at the Tampere University of Technology in Finland in collaboration with our laboratory and the UCLA Laboratory of Neuroimaging. * Raw data diagnostics - An R program that reads in a 4-D data file and provides a diagnostic report. * Code to run various tasks used in the lab - all of these require MATLAB and the MATLAB Psychophysics toolbox: * - Stop signal task (for behavioral testing outside the scanner) * - File Stop signal task (for use in the scanner) * - File mixed gambles task (demo and scanning script)

Proper citation: Poldracklab Portal (RRID:SCR_002712) Copy   

•   Source: SciCrunch Registry

https://github.com/SciCrunch/RRID-Instruments/blob/main/PDF/SCR_002677.pdf

Digital image processing system where microscope settings and processing steps may be adjusted in single user interface. Can acquire images from variety of cameras. Includes software package for capturing, archiving and preparing images for publication. Allows users to visualize and present images in several dimensions. Functionality of imaging toolbox expands constantly with wide range of different modules that are tailored to specific applications or microscope accessories.

Proper citation: Zeiss: AxioVision Imaging System (RRID:SCR_002677) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.graphpad.com/

Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.

Proper citation: GraphPad Prism (RRID:SCR_002798) Copy   

•   Source: SciCrunch Registry

http://www.phalanxbiotech.com/

Group service that provides expression profiling products and services. They manufacture DNA microarrays for gene expression and microRNA profiling.

Proper citation: Phalanx Biotech Group (RRID:SCR_002717) Copy   

•   Source: SciCrunch Registry

http://reflect.embl.de/

Web service that tags gene, protein, and small molecule names in any web page. Clicking on a tagged term opens a small popup showing summary information, and allows the user to quickly link to more detailed information. For each protein or gene, Reflect provides domain structure, sub-cellular localization, 3D structure, and interaction partners. For small molecules, it provides the chemical structure and interaction partners. Reflect can be installed as a plugin to Firefox or Internet Explorer, or can be used by entering a URL in the field provided. It can also be accessed programmatically via a REST or SOAP API, and a Reflect button can easily be added to any web page using Javascript or using a CGI proxy. Reflect was first-prize winner out of over 70 submissions in the Elsevier Grand Challenge, an international competition for systems that improve the way scientific information is communicated and used. Reflect can be edited and improved by the community.

Proper citation: Reflect (RRID:SCR_002714) Copy   

•   Source: SciCrunch Registry

http://www.osti.gov/

The Office of Scientific and Technical Information's mission is to advance science and sustain technological creativity by making R&D findings available and useful to Department of Energy (DOE) researchers and the public. At OSTI you can find research results and science information from the Manhattan Project to the present, download documents, view energy citations, discover patents and e-prints, read about ongoing research projects and amazing accomplishments, search science conference proceedings and software, and connect to U.S. and global science portals. You can do this by using special online tools, such as: * Key Resources * DOE Science Accelerator * Science.gov * WorldWideScience.org Strategies for accomplishing the OSTI mission: * Collaborate within DOE through the Scientific and Technical Information Program to develop and maintain efficient, state-of-the-art access and delivery of research results. * Partner with others to facilitate alliances for national and international cooperation and information exchange. * Develop, deliver, and maintain customized information products and services for a variety of constituencies. * Implement Department-wide STI policy and best business practices. * Preserve STI, in tangible copies or electronically, as appropriate. * Accelerate the diffusion of knowledge to advance science. OSTI develops and maintains search tools that use a special technology called federated search. KEY RESOURCES Research Documents/Information Information Bridge Find DOE R&D full-text documents and bibliographic citations. DOE R&D Accomplishments Find information about the outcomes of past DOE R&D. DOE patents Find patents resulting from DOE-sponsored research and development. E-print Network Find e-prints in basic and applied sciences . Energy Citations Database (ECD) Find bibliographic records and full-text where available. Adopt-A-Doc? is an on-demand service that provides individuals the option to sponsor the digitization of full-text DOE technical reports. Science Conference Proceedings Find select science and technology conference papers and proceedings. EnergyFiles Find databases and websites of interest to DOE. Research Summaries DOE R&D Project Summaries Find R&D projects underway at DOE. Federal R&D Project Summaries Find R&D projects underway at federal agencies. Science Information from U.S. Agencies Science.gov Find selected science information provided by U.S. Government agencies. Science Information from Global Sources WorldWideScience.org Find science from participating nations of every inhabited continent. ETDEWEB Register for access to worldwide energy technology discoveries. International Nuclear Information System Find International bibliographic records related to peaceful applications of nuclear science and technology. Science Education Resources ScienceLab A portal listing numerous education resources within DOE and beyond Scientific Research Data About Scientific Research Data Learn about the Department of Energys data discovery tool as well as data centers, forums, and publications. DOE Data Explorer Find scientific research data - such as computer simulations, numeric data files, figures and plots, interactive maps, multimedia, and scientific images - generated in the course of DOE-sponsored research in various science disciplines. Scientific and Technical Software Energy Science and Technology Software Center Find federally funded scientific and technical software developed by the national laboratories, other facilities and DOE contractors. SCIENCE ACCELERATOR Science Accelerator is a gateway to science, including R&D results, project descriptions, accomplishments, and more, via resources made available by the Office of Scientific and Technical Information (OSTI), U.S. Department of Energy. Science Accelerator was developed and is made available by OSTI as a free public service. SCIENCE.GOV Science.gov searches over 40 databases and 1,950 selected websites, offering 200 million pages of authoritative U.S. government science information, including research and development results. WORLDWIDESCIENCE.ORG WorldWideScience.org is a global science gatewayaccelerating scientific discovery and progress through a multilateral partnership to enable federated searching of national and international scientific databases and portals.

Proper citation: Office of Scientific and Technical Information (RRID:SCR_002670) Copy   

•   Source: SciCrunch Registry

http://camera.calit2.net/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data.

Proper citation: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (RRID:SCR_002676) Copy   

•   Source: SciCrunch Registry

http://www.unidesign.ch/wiki/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 6, 2012. Connectome Wiki is a knowledge base for macro- and mesoscale brain region and brain structural connectivity information across species. Employing modern semantic wiki technology, it serves as collaborative platform as well. What can I get? * Brain Regions: Plenty of information, including links to relevant literature and much more. * Brain Connections: Well established neuronal connections based mainly on neuronal tracer studies from the literature. * Abbreviations: Look up abbreviations and corresponding English and Latin names * Partition Schemes: Foundational and more partitions with their corresponding delineation criteria and protocols. * Species: Information about different species is available, using their binomial name as identifier. * External: Enhance the ConnectomeViewer with Volume-To-Ontology mappings. * Data Source: You can download the raw data in RDF or JSON. How can I contribute? If your research is in particular brain regions, or model organisms not yet registered, feel free to act as domain expert and add your knowledge. If you do any tracer studies, add findings with appropriate published papers. Incrementally building a mesoscale skeleton wiring diagram. Complete anything that is missing. See also PapersToAdd. Register your own partition scheme and link it semantically against known schemes. Adding brain region pages for your particular research organisms. Use ConnectomeWiki as knowledge backend for your application concerned with gross neuroanatomy. The goals of this wiki are: * A collaborative platform to collect, collate, manage and disseminate mesoscale nervous system region and connectivity information across various species * Authority for Brain Region Abbreviations * Representation of Brain Region Homologies * Interrelation of Brain Partition Schemes * Information source for the ConnectomeViewer application

Proper citation: Connectome Wiki (RRID:SCR_002675) Copy   

•   Source: SciCrunch Registry

https://github.com/alibashir/pacmonstr

Software that implements a reference-based probabilistic approach to identify the Tandem Repeat (TR) region and estimate the number of these TR elements in long DNA reads.

Proper citation: PacmonSTR (RRID:SCR_002796) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/ropebwt2

A software tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This algorithm can be largely considered a mixture of BCR and dynamic FM-index. Nonetheless, ropeBWT2 is unique in that it may implicitly sort the input into reverse lexicographical order (RLO) or reverse-complement lexicographical order (RCLO) while building the index.

Proper citation: RopeBWT2 (RRID:SCR_002673) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/safa

A software package that anayzes the structral details of RNA molecules through rapid quantification of a footprinting gel. By automating many of the steps involved in gel analysis, approximately one entire gel with thousands of bands can be quantified in less than 10 minutes using SAFA. In general, all the automated features have a manual override, such that even difficult or exceptional gels can be analyzed with the package.

Proper citation: SAFA Footprinting Software (RRID:SCR_002707) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.wanprc.org/

Center that aims to provide an environment to support biomedical research directed towards human health issues and nonhuman primate health and biology. To meet this mission, the WaNPRC supports biomedical research activities, professional research staff, specifically bred and maintained nonhuman primate colonies, and dedicated facilities and equipment required for nonhuman primate research protocols.

Proper citation: Washington National Primate Research Center (RRID:SCR_002761) Copy   

•   Source: SciCrunch Registry

https://github.com/ahmohamed/NetPathMiner

Software that implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats (KGML, SBML and BioPAX), enabling its utility to most common pathway databases. In addition, it provides different visualization techniques to facilitate the analysis of even thousands of output paths.

Proper citation: NetPathMiner (RRID:SCR_002757) Copy   

•   Source: SciCrunch Registry

http://yu68.github.io/GATE/

Model-based, open source software analysis tool for chromatin states prediction based on time-course epigenetic marks data. It uses a combinatory Finite Mixture model nested with HMM to model the time course marks data in which each single hidden markov model describes the hidden states for a region set across different time points.

Proper citation: GATE (RRID:SCR_002756) Copy   

•   Source: SciCrunch Registry

http://www.mendeley.com/

Web application as free reference manager and academic social network to organize your research, collaborate with others online, and discover the latest research. Automatically generate bibliographies, Collaborate easily with other researchers online, Easily import papers from other research software, Find relevant papers based on what you're reading, Access your papers from anywhere online, Read papers on the go with the iPhone app. The software, Mendeley Desktop, offers: * Automatic extraction of document details * Efficient management of your papers * Sharing and synchronization of your library (or parts of it) * Additional features: A plug-in for citing your articles in Microsoft Word, OCR (image-to-text conversion, so you can full-text search all your scanned PDFs), etc The website, Mendeley Web, complements Mendeley Desktop by offering these features: * An online back up of your library * Statistics of all things interesting * A research network that allows you to keep track of your colleagues' publications, conference participations, awards etc * A recommendation engine for papers that might interest you.

Proper citation: Mendeley (RRID:SCR_002750) Copy   

•   Source: SciCrunch Registry