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http://lincsportal.ccs.miami.edu/dcic-portal/

Portal which provides a unified interface for searching LINCS dataset packages and reagents. Users can use the portal to access datasets, small molecules, cells, genes, proteins and peptides, and antibodies.

Proper citation: LINCS Data Portal (RRID:SCR_014939) Copy   

•   Source: SciCrunch Registry
  

http://iclac.org

An independent committee established to improve visibility of cell lines and promote awareness and authentication testing to combat false or misidentified cell lines. It contains a databases of cross-contaminated or otherwise misidentified cell lines, as well as resources to familiarize users of cell lines and the problem of misidentification. Their Terms of Reference defines false or misidentified cell lines and other commonly used terms, as well as sets out the committee goals and ground rules.

Proper citation: International Cell Line Authentication Committee (RRID:SCR_014414) Copy   

•   Source: SciCrunch Registry
  

http://www.researchconnection.com

THIS RESOURCE IS NO LONGER IN SERVICE. Documented June 21, 2018.

A service resource and collaboration tool which connects academically affiliated researchers to undergraduate and graduate students. Researchers can advertise their lab and open positions as well as organize and manage applicants. Students can browse labs based on university and field(s) of interest and apply directly for lab positions or jobs. Universities must officially partner with ResearchConnection to advertise labs.

Proper citation: ResearchConnection (RRID:SCR_013965) Copy   

•   Source: SciCrunch Registry
  

https://singlecell.broadinstitute.org/single_cell

Portal specializes in visualizing and disseminating single cell data. Allows you to use natural language and faceted search to discover other scientists’ research and share your own findings. Each study includes information on cell types, singular or multiple gene expression, and spatial transcriptomics. Interactive visualizations allow to explore cell clusters and search for related genes.

Proper citation: Single Cell Portal (RRID:SCR_014816) Copy   

•   Source: SciCrunch Registry
  

http://becs.aalto.fi/en/research/bayes/drifter/

Model based Bayesian method for eliminating physiological noise from fMRI data. This algorithm uses image voxel analysis to isolate the cardiac and respiratory noise from the relevant data.

Proper citation: DRIFTER (RRID:SCR_014937) Copy   

•   Source: SciCrunch Registry
  

https://grade.bsc.gwu.edu/web/grade/home

A comparative study that aims to determine which combination of two medications is best for glycemic control in Type 2 Diabetes, has the fewest side effects, and is the most beneficial for overall health. GRADE is a randomized clinical trial of participants diagnosed with type 2 diabetes within the past 10 years who are already on metformin. Participants will be randomly assigned to 1 of 4 commonly-used glucose-lowering drugs (glimepiride, sitagliptin, liraglutide, and basal insulin glargine), plus metformin, and will be followed for up to 7 years.

Proper citation: Glycemic Reduction Approaches in Diabetes: A Comparative Effectiveness Study (GRADE) (RRID:SCR_014384) Copy   

•   Source: SciCrunch Registry
  

https://www.janelia.org/confocal-imagery-management-and-analysis-tools

A discovery platform used to analyze and annotate imagery for individual projects, while assembling shared data resources. It was originally applied to Drosophila neuronal anatomy and neuroblast lineage analysis and is currently being extended to support mouse whole-brain projection tracing. The Workstation is both a pipeline management system that extracts entities from 3D imagery and a suite of tools that enable scientists to annotate large imagery datasets. A Entity-Attribute-Value (EAV) graph permits any element to be annotated by users with custom ontologies. By allowing any entity to have multiple parents, the graph can be re-arranged by each user without copying the underlying image data.

Proper citation: Janelia Workstation (RRID:SCR_014302) Copy   

•   Source: SciCrunch Registry
  

http://www.3dhistech.com/pannoramic_viewer

Software tool as a digital virtual microscope for viewing and moving scanned histological slides and for making annotations and measurements on them. Used in digital pathology. Helps to simplify the areas of the pathology workflow where imaging, slide digitization, storage, archivation, visualization and analysis are performed.

Proper citation: Pannoramic Viewer (RRID:SCR_014424) Copy   

•   Source: SciCrunch Registry
  

http://ambermd.org/

Software package of molecular simulation programs. It is distributed into AmberTools15 and Amber14. AmberTools15 is a software package which can carry out complete molecular dynamics simulations with either explicit water or generalized Born solvent models. It is distributed in source code format and must be compiled in order to be used. Amber14 builds on AmberTools15 by adding the pmemd program, which provides better performance on multiple CPUs and dramatic speed improvements on GPUs compared to sander (molecular dynamics). GPU info, manuals, and tutorials are available on the website.

Proper citation: Assisted Model Building with Energy Refinement (AMBER) (RRID:SCR_014230) Copy   

•   Source: SciCrunch Registry
  

http://sharedresources.fredhutch.org/core-facilities/cceh-administration

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July,27,2022. Core facility that provides scientific and budgetary oversight for all CCEH activities. This includes training programs, high school summer internships, and and pilot and feasibility program for new projects.

Proper citation: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology (RRID:SCR_015320) Copy   

•   Source: SciCrunch Registry
  

http://snap-graph.sourceforge.net

SNAP (Small-world Network Analysis and Partitioning) is an extensible parallel framework for exploratory analysis and partitioning of large-scale networks. SNAP is implemented in C, uses OpenMP primitives for parallelization, and targets sequential, multicore, and symmetric multiprocessor platforms. Our intent with SNAP is to provide a simple and intuitive interface for network analysis and application design, hiding the parallel programming complexity from the user. In addition to path-based, centrality, and community identification queries on large-scale graphs, we support commonly-used preprocessing kernels and quantitative measures that help understand the global network topology. The latest version of SNAP (0.4) was released in August 2010. Sponsors: This work was supported in part by NSF Grants CAREER CCF-0611589, NSF DBI-0420513, ITR EF/BIO 03-31654, IBM Faculty Fellowship and Microsoft Research grants, NASA grant NP-2005-07-375-HQ, and DARPA Contract NBCH30390004. Keywords: network, analysis, software, graph, traversal, betweenness centrality, community, identification, multicore,

Proper citation: Small-world Network Analysis and Partitioning (RRID:SCR_013662) Copy   

•   Source: SciCrunch Registry
  

http://www.med.umich.edu/mgpc/

Center whose goal is to investigate signal transduction mechanisms regulating homeostasis and GI disorders. Their approach includes studies on genetics and gene regulation, cellular signaling pathways, receptors and ion channels.

Proper citation: University of Michigan Center for Gastrointestinal Research (RRID:SCR_015605) Copy   

•   Source: SciCrunch Registry
  

https://commonfund.nih.gov/metabolomics/index

A US national program which supoorts the development of technologies in order to enhance the metabolomics field. It specifically increases the national metabolomics research capacity by supporting five core programs: Training in Metabolomics, Metabolomics Technology Development, Metabolomics Reference Standard Synthesis, Metabolomics Data Sharing and International Collaboration, and Comprehensive Metabolomics Resource Cores.

Proper citation: NIH Metabolomics program (RRID:SCR_014634) Copy   

•   Source: SciCrunch Registry
  

https://github.com/MikkelSchubert/paleomix

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software toolkit for the processing of ancient and modern HTS data. PALEOMIX also aids in metagenomic analysis of the extracts from the HTS processing.

Proper citation: PALEOMIX (RRID:SCR_015057) Copy   

•   Source: SciCrunch Registry
  

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

A semi-automated software tool for dental plaque biofilm quantification in quantitative light-induced fluorescence (QLF) images.

Proper citation: BiofilmQuant (RRID:SCR_014088) Copy   

•   Source: SciCrunch Registry
  

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

Data sets from the atlasing of the basal ganglia (ATAG) consortium, which provides ultra-high resolution 7Tesla (T) magnetic resonance imaging (MRI) scans from young, middle-aged, and elderly participants. They include whole-brain and reduced field-of-view MP2RAGE and T2 scans with ultra-high resolution at a sub millimeter scale. The data can be used to develop new algorithms that help building new high-resolution atlases both in the basic and clinical neurosciences. They can also be used to inform the exact positioning of deep-brain electrodes relevant in patients with Parkinsons disease and neuropsychiatric diseases.

Proper citation: 7T Structural MRI scans ATAG (RRID:SCR_014084) Copy   

•   Source: SciCrunch Registry
  

http://sgdp.iop.kcl.ac.uk/opcrit/

The operational criteria OPCRIT checklist for psychotic and affective illness has been designed to facilitate a polydiagnostic approach to mental illness. The package is specifically for the needs of the researcher and is intended to be used by clinicians or investigators trained in clinical research. It is not recommended for use by raters without previous experience in psychopathology and psychiatric diagnosis. Click the Download link below to download Opcrit. This download is compressed zip file which will yield the actual installer files. Open WinopInstallerFiles.zip and when prompted extract the contents to a temporary location. One of the files extracted is Setup.exe. Run this setup file and follow the instructions to install the Opcrit. Depending on your system type and version of Windows, you may need to reboot your system once installation is complete. After installation, you will also need to download and run the installer for the october 2009 update (see below).

Proper citation: Operational Criteria (RRID:SCR_013359) Copy   

•   Source: SciCrunch Registry
  

http://doa.nubic.northwestern.edu/pages/search.php

Project portal for a collaborative database aiming to provide a comprehensive annotation to human genome.It uses the computable, controlled vocabulary of Disease Ontology (DO) and NCBI Gene Reference Into Function (GeneRIF).

Proper citation: DOAF (RRID:SCR_015666) Copy   

•   Source: SciCrunch Registry
  

http://pa.wishartlab.com/pa/pa/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Web-based tool that predicts subcellular localization and GO molecular function of proteins. Proteome Analyst has the ability to explain its predictions and gives users the ability to run a large set of tools on their proteins.

Proper citation: Proteome Analyst (RRID:SCR_013807) Copy   

•   Source: SciCrunch Registry
  

http://www.rhino3d.com/features

3D modeling software used to create, edit, analyze, document, render, animate, and translate surfaces, solids, point clouds, and polygon meshes. It can also be used to analyze and manufacture a variety of products.

Proper citation: Rhinoceros (RRID:SCR_014339) Copy   

•   Source: SciCrunch Registry