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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.
Open source designs for customizable, MRI compatible microdrive capable of positioning probes including stimulating electrodes, recording electrodes, drug cannulae, or optogenetic fibers within brain. Design integrates cranial implant, penetration grid for guiding probes, and microdrive body assembly with actuators. Used by neuroscience community related to electrical microstimulation, neuronal recording, and local drug delivery.
Proper citation: MRI Compatible and Customizable Microdrive Design for Neuroscience Research (RRID:SCR_019247) Copy
Software pipeline for single-nucleus RNAseq data generated by Smart-seq2 assays.Used to simultaneously process multiple libraries of single nuclei Smart-seq2 and Smart-seq4 data. For each library (nucleus), the pipeline trims paired FASTQ files, aligns trimmed reads to the genome, counts intronic and exonic reads, and calculates quality control metrics. Counts and metrics for all libraries are combined into merged Loom formatted count matrix.
Proper citation: Smart-seq2 Single Nucleus Multi Sample Pipeline (RRID:SCR_021312) Copy
Open community of researchers, educators, and professionals with goal of improving way we develop, share, use, and re-use agent based and computational models for study of social and ecological systems. Develops and maintains CoMSES Model Library, digital repository that supports discovery and good practices for software citation, digital preservation, reproducibility, and reuse.
Proper citation: CoMSES Net (RRID:SCR_017598) Copy
https://edspace.american.edu/openbehavior/project/autopilot/
Project related to behavioral experiments.Provides software Python framework for running behavioral experiments designed by University of Oregon scientists.
Proper citation: AutoPilot project (RRID:SCR_021448) Copy
Library with storage capacity of over million compounds possessing diversified structures. Coupled with this library will be advanced sample handling, information management and quality control systems. As important material and information resource, CNCL will work with both domestic and international stakeholders to promote sustained development of Chinese pharmaceutical industry.
Proper citation: Chinese National Compound Library (RRID:SCR_018723) Copy
https://github.com/ENCODE-DCC/chip-seq-pipeline2/
Software tool as ChIP-seq pipeline for processing ChIP-seq reads, aligning to reference genome, peak calling, and IDR analysis of replicate data according to ENCODE standards.
Proper citation: ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline (RRID:SCR_021323) Copy
https://www.southernbiotech.com/
Commercial antibody company that focuses on the development, production, purification, conjugation, and commercialization of antibodies.
Proper citation: SouthernBiotech (RRID:SCR_019250) Copy
A manufacturer of early discovery research products including antibodies, recombinant proteins, ELISA kits, second step reagents and other life sciences products.
Proper citation: Leinco Technologies (RRID:SCR_019252) Copy
Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images.
Proper citation: QuPath (RRID:SCR_018257) Copy
Open knowledge base that can be read and edited by both humans and machines. Storage for structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. Provides support to many other sites and services beyond just Wikimedia projects.
Proper citation: Wikidata (RRID:SCR_018492) Copy
Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis.
Proper citation: hMRI-toolbox (RRID:SCR_017682) Copy
Open source software Python package for working with hierarchical data. Provides APIs for specifying data models, reading and writing data to different storage backends, and representing data with Python object.Used for working with standardizing, reading, and writing hierarchical object data.
Proper citation: Hierarchical Data Modeling Framework (RRID:SCR_021303) Copy
https://www.nest-initiative.org
Incorporated as non-profit member based organization promoting scientfic collaboration in computational neuroscience.Advances computational neuroscience by pushing limits of large scale simulations of biologically realistic neuronal networks.
Proper citation: NEST Initiative (RRID:SCR_020978) Copy
https://github.com/berenslab/mini-atlas
Phenotypic variation of transcriptomic cell types in mouse motor cortex.Repository contains analysis code and preprocessed data.Data includes exonic and intronic gene counts, extracted electrophysiological features, extracted morphological features and z-profiles. Datasets with recorded at room temperature and recorded at physiological temperature.
Proper citation: BarensLab Mini-Atlas (RRID:SCR_021115) Copy
The Smart-seq2 Single Nucleus Multi-Sample (Multi-snSS2) pipeline was developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) to process single-nucleus RNAseq (snRNAseq) data generated by Smart-seq2 assays.
Proper citation: Smart-seq2 Multi-Sample Pipeline (RRID:SCR_018920) Copy
https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/balbes/balbes_layout.html
Software system for solving protein structures using x-ray crystallographic data. Automatic molecular replacement pipeline for molecular replacement in CCP4. Integrates into one system all components necessary for solving crystal structure by Molecular Replacement. System is automated so that it needs no user intervention when running combination of jobs such as model searching, molecular replacement and refinement.
Proper citation: BALBES (RRID:SCR_018763) Copy
https://github.com/NeLy-EPFL/DeepFly3D
Software tool as PyTorch and PyQT5 implementation of 2D-3D tethered Drosophila pose estimation. Image annotation tool used for pose estimation and appendage tracking. Provides interface for pose estimation and to permit further correction of 2D pose estimates, which are automatically converted to 3D pose.
Proper citation: DeepFly3D (RRID:SCR_021402) Copy
https://edspace.american.edu/openbehavior/project/argus/
Portal provides software tool for analysis and quantification of both single and socially interacting zebrafish. Software data extraction and analysis tool built in open source R language for tracking zebrafish behavior.
Proper citation: Argus (RRID:SCR_021585) Copy
Software to detect regions of interests and distinguishes cells and sub-cellular objects within these target regions from immunohistochemistry specimen. Used for digital pathology image analysis.
Proper citation: Tissue Studio (RRID:SCR_023001) Copy
https://bbp.epfl.ch/nmc-portal/welcome.html
Neocortical microcircuit collaboration portal is resource for rat somatosensory cortex. NMC portal allows users to access experimental data used in reconstruction process, download cellular and synaptic models, and analyze predicted properties of microcircuit.
Proper citation: Neocortical Microcircuit Portal (RRID:SCR_022032) Copy
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