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http://www.bioconductor.org/packages/release/bioc/html/qvalue.html

R package that takes a list of p-values resulting from the simultaneous testing of hypotheses and estimates their q-values. It is designed to measure the proportion of false positives when a test is significant. The software is capable of generating plots for visualization. It can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

Proper citation: Qvalue (RRID:SCR_001073) Copy   

•   Source: SciCrunch Registry

http://www.frontiersin.org/10.3389/conf.fninf.2013.09.00111/event_abstract

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. ASP.NET AJAX .NET 4, Telerik controls enabled application designed to be used with the books presented, papers and web content to help with the acceleration of learning and software development for the neurosciences. All content developed at The Cromwell Workshop is intended to accelerate the implementation of biomedical knowledge, help with EEG clinical certifications and provide the opportunity for students, software developers, neuroscientists, neurologists and neurosurgeons to collaborate globally with knowledge content. e-NeoTutor relies on a subscription model to build software components in multiple languages and access book material. Tutor designed to complement free online course content in neuroscience, work with the Society of Neuroscience, The Human Connectome Project and assist researchers with CNIM certification, biomedical informatics, neuroinformatics and neuroscience training programs.

Proper citation: eNeoTutor (RRID:SCR_001590) Copy   

•   Source: SciCrunch Registry

https://rubyonrails.org/

Open source web application development framework. Model View Controller framework, providing default structures for database, web service, and web pages.

Proper citation: Ruby on Rails (RRID:SCR_022129) Copy   

•   Source: SciCrunch Registry

https://ptc.bocsci.com/services/protein-ubiquitination-services.html

Service in field of drug discovery and research. BOC Sciences service in one stop Proteolysis Targeting Chimeric based molecular drug discovery which has become strategy in area of drug discovery.

Proper citation: BOC Sciences Protein Ubiquitination Service Resource (RRID:SCR_022127) Copy   

•   Source: SciCrunch Registry

https://ptc.bocsci.com/services/small-molecule-target-protein-ligand.html

Provides small molecule target protein ligand service to customers to meet new drug discovery goals.

Proper citation: BOC Sciences Small molecule target protein ligand Service Resource (RRID:SCR_022126) Copy   

•   Source: SciCrunch Registry

https://ptc.bocsci.com/services/peptide-ligand-for-target-protein.html

Service provider in drug discovery and development. Provides one stop PROTA development, which has become strategy in field of small molecular drug discovery. Provides peptide ligand design for target protein to customers to meet new drug discovery goals.

Proper citation: BOC Sciences Peptide ligand for target protein Service Resource (RRID:SCR_022125) Copy   

•   Source: SciCrunch Registry

http://toppcluster.cchmc.org/

A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene.

Proper citation: ToppCluster (RRID:SCR_001503) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/viste/

Open source, platform-independent application for the visualization and analysis of complex, high-dimensional imaging data such as Diffusion Tensor Imaging (DTI) and High Angular Resolution Diffusion Imaging (HARDI). It has a plugin-based architecture which allows third parties to develop new plugins to extend the tool. Overview of the many features: * vIST/e is programmed in C++. It uses the Visualization Toolkit for visualization and pipelined data processing, as well as the cross-platform toolkit Qt Framework for an easy-to-use Graphical User Interface. * vIST/e introduces a powerful new plugin system, which allows for modular development with increased extensibility and stability. * Powerful GPU-based visualization techniques allow for smooth, real-time visualization of large data sets. Using custom ray tracing algorithms created with OpenGL, vIST/e can render DTI ellipsoids and HARDI spherical harmonics glyphs up to 4th order. The high frame rates offered by modern GPU technology allows for interactive exploration of this complex data. * Diffusion Tensor Imaging data can be visualized and interactively explored in a number of ways, including multiple cross-sections, volume rendering, and tensor glyphs. Derived scalar volumes, including various different anisotropy measures, can be computed and visualized. Data from other modalities, such as structural MRI, can be shown alongside the DTI data. * Various fiber tracking methods allow for fast and accurate reconstruction of fiber pathways. Interactively defined Regions of Interest (ROIs) can be used for seeding and filtering of fibers. Fibers are visualized either as lines, optionally using a powerful, GPU-based lighting engine, or as 3D structures such as tubes. * Scalar volumes, glyphs, and fibers can be colored using a wide array of coloring option. Customizable color loop-up tables allow for highly flexible visualization of scalar data. * Visualization and processing of various different HARDI formats is supported. HARDI data is interactively visualized using highly detailed glyphs rendered on the GPU. HARDI glyphs can be visualized in combination with DTI glyphs, for a better overview of complex diffusion data. * vIST/e includes support for NVIDIA's Compute Unified Device Architecture (CUDA), which enables highly parallel, GPU-based data processing, allowing for significant speed-up of computationally expensive algorithms.

Proper citation: vIST/e (RRID:SCR_001627) Copy   

•   Source: SciCrunch Registry

http://coins.mrn.org/

A web-based neuroimaging and neuropsychology software suite that offers versatile, automatable data upload/import/entry options, rapid and secure sharing of data among PIs, querying and export all data, real-time reporting, and HIPAA and IRB compliant study-management tools suitable to large institutions as well as smaller scale neuroscience and neuropsychology researchers. COINS manages over over 400 studies, more than 265,000 clinical neuropsychological assessments, and 26,000 MRI, EEG, and MEG scan sessions collected from 18,000 participants at over ten institutions on topics related to the brain and behavior. As neuroimaging research continues to grow, dynamic neuroinformatics systems are necessary to store, retrieve, mine and share the massive amounts of data. The Collaborative Informatics and Neuroimaging Suite (COINS) has been created to facilitate communication and cultivate a data community. This tool suite offers versatile data upload/import/entry options, rapid and secure sharing of data among PIs, querying of data types and assessments, real-time reporting, and study-management tools suitable to large institutions as well as smaller scale researchers. It manages studies and their data at the Mind Research Network, the Nathan Kline Institute, University of Colorado Boulder, the Olin Neuropsychiatry Research Center (at) Hartford Hospital, and others. COINS is dynamic and evolves as the neuroimaging field grows. COINS consists of the following collaboration-centric tools: * Subject and Study Management: MICIS (Medical Imaging Computer Information System) is a centralized PostgreSQL-based web application that implements best practices for participant enrollment and management. Research site administrators can easily create and manage studies, as well as generate reports useful for reporting to funding agencies. * Scan Data Collection: An automated DICOM receiver collects, archives, and imports imaging data into the file system and COINS, requiring no user intervention. The database also offers scan annotation and behavioral data management, radiology review event reports, and scan time billing. * Assessment Data Collection: Clinical data gathered from interviews, questionnaires, and neuropsychological tests are entered into COINS through the web application called Assessment Manager (ASMT). ASMT's intuitive design allows users to start data collection with little or no training. ASMT offers several options for data collection/entry: dual data entry, for paper assessments, the Participant Portal, an online tool that allows subjects to fill out questionnaires, and Tablet entry, an offline data entry tool. * Data Sharing: De-identified neuroimaging datasets with associated clinical-data, cognitive-data, and associated meta-data are available through the COINS Data Exchange tool. The Data Exchange is an interface that allows investigators to request and share data. It also tracks data requests and keeps an inventory of data that has already been shared between users. Once requests for data have been approved, investigators can download the data directly from COINS.

Proper citation: Mind Research Network - COINS (RRID:SCR_000805) Copy   

•   Source: SciCrunch Registry

https://github.com/Benson-Genomics-Lab/TRF

Software tool to locate and display tandem repeats in DNA sequences. Program to analyze DNA sequences.

Proper citation: Tandem Repeats Finder (RRID:SCR_022193) Copy   

•   Source: SciCrunch Registry

https://github.com/bwa-mem2/bwa-mem2

Software tool for sequence mapping.The next version of BWA-MEM. Used for aligning sequencing reads against large reference genome.

Proper citation: BWA-MEM2 (RRID:SCR_022192) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/us/en/home/life-science/cell-analysis/cellular-imaging/evos-cell-imaging-systems/models/evos-xl-core.html?ef_id=Cj0KCQjwpImTBhCmARIsAKr58cwB-d2Yr5yUaQuJlpybgp8ywZnlsAUkt4VcZMv6TTE7czxdnzJlVOgaAiv5EALw_wcB:G:s&s_kwcid=AL!3652!3!586406505002!p!!g!!evos%20xl&cid=bid_pca_iie_r01_co_cp1359_pjt0000_bid00000_0se_gaw_bt_lgn_ins&gclid=Cj0KCQjwpImTBhCmARIsAKr58cwB-d2Yr5yUaQuJlpybgp8ywZnlsAUkt4VcZMv6TTE7czxdnzJlVOgaAiv5EALw_wcB

Designed to eliminate complexities of microscopy, EVOS XL Core system captures high-quality brightfield cell images right at your benchtop within minute. Instrument for monitoring cell cultures, either within hood or in cell culture room.

Proper citation: Thermo Fisher: EVOS XL Core Imaging System (RRID:SCR_022190) Copy   

•   Source: SciCrunch Registry

http://statalign.github.io/

Software package for Bayesian analysis of protein, DNA and RNA sequences. It utilizes multiple alignments, phylogenetic trees and evolutionary parameters to quantify uncertainty in these analyses. It is written in Java.

Proper citation: StatAlign (RRID:SCR_001892) Copy   

•   Source: SciCrunch Registry

https://jwst.nasa.gov/content/observatory/instruments/nircam.html

Instrument aboard the James Webb Space Telescope. It has two major tasks, as imager from 0.6 to 5 micron wavelength, and as wavefront sensor to keep 18-section mirrors functioning as one. Imager covers infrared wavelength range 0.6 to 5 microns. NIRCam detects light from the earliest stars and galaxies in process of formation, population of stars in nearby galaxies, as well as young stars in Milky Way and Kuiper Belt objects. NIRCam is equipped with coronagraphs, instruments that allow astronomers to take pictures of very faint objects around central bright object, like stellar systems.

Proper citation: Near Infrared Camera (RRID:SCR_022113) Copy   

•   Source: SciCrunch Registry

https://www.creative-peptides.com/

Creative peptides is specialized in process development and manufacturing of bioactive peptides.Offers custom peptide synthesis, process development, manufacturing as well as catalog products for customers in industry and research area. Creative Peptides is staffed by scientific teams with experts in the fields of peptide technology, antibodies and synthetic chemistry.

Proper citation: Creative Peptides (RRID:SCR_022112) Copy   

•   Source: SciCrunch Registry

http://www.ruffus.org.uk

Software lightweight Python library for computational pipelines. Reproducible pipeline framework.

Proper citation: Ruffus (RRID:SCR_022196) Copy   

•   Source: SciCrunch Registry

https://github.com/marbl/MashMap

Software tool as fast approximate aligner for long DNA sequences. Used for computing local alignment boundaries between long DNA sequences.

Proper citation: MashMap (RRID:SCR_022194) Copy   

•   Source: SciCrunch Registry

https://github.com/QMICodeBase/TORTOISEV4

An integrated and flexible software package for processing of DTI data, and in general for the correction of diffusion weighted images to be used for DTI and potentially for high angular resolution diffusion imaging (HARDI) analysis. It can be run on both Linux and Mac platforms. It is composed of two modules named DIFF PREP and DIFF CALC. * DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space * DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis In addition, TORTOISE contains additional Utilities, such as a tool for the analysis of multi-center phantom data.

Proper citation: TORTOISE (RRID:SCR_001645) Copy   

•   Source: SciCrunch Registry

http://gmdd.shgmo.org/Computational-Biology/GRS/

A compression tool for efficient storage of Genome Re-Sequencing data. GRS processes genome sequence data without use of reference SNPs and other variants. It can also automatically rebuild the individual genome sequence data using the reference genome sequence.

Proper citation: GRS (RRID:SCR_001008) Copy   

•   Source: SciCrunch Registry

http://www.nactem.ac.uk/facta/

Text mining tool to discover associations between biomedical concepts from MEDLINE articles. Use the service from your browser or via a Web Service. The whole MEDLINE corpus containing more than 20 million articles is indexed with an efficient text search engine, and it allows you to navigate such associations and their textual evidence in a highly interactive manner - the system accepts arbitrary query terms and displays relevant concepts immediately. A broad range of important biomedical concepts are covered by the combination of a machine learning-based term recognizer and large-scale dictionaries for genes, proteins, diseases, and chemical compounds. There is also a FACTA+ visualization service that can be found here: http://www.nactem.ac.uk/facta-visualizer/

Proper citation: FACTA+. (RRID:SCR_001767) Copy   

•   Source: SciCrunch Registry