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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://amp.pharm.mssm.edu/LJP/
Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations.
Proper citation: LINCS Joint Project - Breast Cancer Network Browser (RRID:SCR_016181) Copy
https://github.com/ihmwg/IHM-dictionary
Software resource for a data representation for integrative/hybrid methods of modeling macromolecular structures.
Proper citation: IHM-dictionary (RRID:SCR_016186) Copy
Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations.
Proper citation: PDB-Dev (RRID:SCR_016185) Copy
Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis.
Proper citation: GOTrack (RRID:SCR_016399) Copy
https://www.icpsr.umich.edu/icpsrweb/content/addep/index.html
Provides access to data including wide range of topics related to disability. ADDEP data can be used to better understand and inform the implementation of Americans with Disabilities Act and other disability policies.
Proper citation: Archive of Data on Disability to Enable Policy (ADDEP) (RRID:SCR_016315) Copy
Supplier of polar lipids.
Proper citation: Avanti Polar Lipids (RRID:SCR_016391) Copy
http://www2.mrc-lmb.cam.ac.uk/relion
Software for determination of cryo-EM structures. It employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy.
Proper citation: RELION (RRID:SCR_016274) Copy
https://hirnetwork.org/project/hirncc
Consortium that provides infrastructure to promote communication and collaboration among current and future HIRN participants, facilitating scientific advances and the sharing of data, tools, and reagents among HIRN members and the research community at large.
Proper citation: HIRN Coordinating Center (RRID:SCR_016395) Copy
Simulation software for improving the performance of real systems. Used for developing, analyzing, and packaging dynamic feedback models.
Proper citation: Vensim (RRID:SCR_016394) Copy
https://ccrod.cancer.gov/confluence/display/ROB2/Home
Software that performs quantitative analysis of angiogenesis. It specializes in quantitative assessment of various vessel morphometric and spatial parameters, including vessel length and density, branching index, lacunarity, etc.
Proper citation: AngioTool (RRID:SCR_016393) Copy
Shared database of multimedia interactions for the study of communication in aphasia.Access to the data in AphasiaBank is password protected and restricted to members of the AphasiaBank consortium group.
Proper citation: AphasiaBank (RRID:SCR_016317) Copy
Software tool for multi-omics data analysis that can perform complex and personalized analysis. Network regulation and molecular mechanism models can be customized according to the requirements of the users.
Proper citation: OmicsBean (RRID:SCR_016322) Copy
http://zzlab.net/blink/index.html
Software for next level of genome wide association studies with both individuals and markers in millions. The method releases the requirement that causative genes are evenly distributed on genome and consequently boosts statistical power.
Proper citation: BLINK (RRID:SCR_016288) Copy
https://github.com/nighres/nighres
Software package for processing of high-resolution neuroimaging data. Nighres is a community-developed project that aims to make neuroscience data tools easier to install, use and extend.
Proper citation: Nighres (RRID:SCR_016287) Copy
https://github.com/Sung-Huan/ANNOgesic
Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.
Proper citation: ANNOgesic (RRID:SCR_016326) Copy
http://www.nitrc.org/projects/longhippsegm/
Software based on robust registration and simultaneous hippocampal segmentation and longitudinal marker classification of brain MRI of an arbitrary number of time points. The framework comprises two parts: a longitudinal segmentation and a longitudinal classification step.
Proper citation: Longitudinal neuroimaging hippocampal markers for diagnosing Alzheimer's disease (RRID:SCR_016282) Copy
https://huttenhower.sph.harvard.edu/humann2
Software for profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data Used for millions of short DNA/RNA reads. This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members.
Proper citation: HUMAnN2 (RRID:SCR_016280) Copy
https://github.com/jbelyeu/SV-plaudit
Software for rapidly curating structural variant (SVs) predictions. SV-plaudit provides a pipeline for creating image views of genomic intervals, automatically storing them in the cloud, deploying a website to view/score them, and retrieving scores for analysis.
Proper citation: SV-plaudit (RRID:SCR_016285) Copy
https://sites.google.com/site/sigenproject/
Software to extract and trace neuronal structure from confocal laser scanning microscope images. It performs the automatic reconstruction of neurons for image stacks and can generate compartmental models of neurons as swc file format data.
Proper citation: SIGEN (RRID:SCR_016284) Copy
https://www.jax.org/jax-mice-and-services
Supplier of mice for research purposes.
Proper citation: JAX Mice and Services (RRID:SCR_016408) Copy
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
