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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.
https://scienceofbehaviorchange.org/about/
Repository for behavioral science measures that have been validated or are in process of being validated in accordance with SOBC Experimental Medicine Approach.
Proper citation: Science of Behavior Change Research Network (RRID:SCR_017385) Copy
https://github.com/lufuhao/GeneSyntenyPipeline
Software pipeline was designed to draw gene synteny plot between genomes and obtain 1 to 1 gene pairs from each genome.
Proper citation: GeneSyntenyPipeline (RRID:SCR_018198) Copy
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp
Brainarray custom CDFs for processing raw Affymetrix data. Used to map probe to probesets. Oligonucleotide probes on GeneChips are reorganized based on latest genome and transcriptome information.
Proper citation: CustomCDF (RRID:SCR_018527) 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://github.com/ttrogers/DecodingDynamic
Data, code, and notebooks for replicating analyses reported in Rogers et al., Evidence for deep, distributed and dynamic semantic code in human ventral anterior temporal cortex.
Proper citation: DecodingDynamic (RRID:SCR_021099) Copy
http://noble.gs.washington.edu/proj/genomedata/
A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems.
Proper citation: Genomedata (RRID:SCR_004544) Copy
http://harvard.eagle-i.net/i/0000012a-2518-fb6c-5617-794280000000
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core provides services: RT PCR service, Gene expression profiling service, Proteomics analysis service, Bioinformatics and Systems Biology analyses, Next Generation Sequencing Service, Affymetrix Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates. Core proteomics facility for the Dana-Farber/Harvard Cancer Center. Workflows and algorithms for analysis of next-generation sequencing data including RNA-Seq, ChIP-Seq, Epigenetics-Seq and DNA seq, Comprehensive workflow for analysis of Microbiome sequencing data, Integrated systems biology analysis of transcriptome, miRNA, epigenome, metabolomics and proteomics data. Pipelines: MALDI Tissue imaging and targeted quantitative proteomics.
Proper citation: Beth Israel Deaconess Medical Center Genomics Proteomics Bioinformatics and Systems Biology Center (RRID:SCR_009668) Copy
https://pynwb.readthedocs.io/en/latest/
Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information.
Proper citation: PyNWB (RRID:SCR_017452) Copy
http://download.ant-neuro.com/matlab/
Software as an EEGLAB tool used for LIBEEP recordings.
Proper citation: Libeep EEGLAB plugin (RRID:SCR_016334) Copy
https://github.com/BioDepot/nbdocker
Software tool as Jupyter Notebook extension for Docker. Each Docker container encapsulates its individual computing environment to allow different programming languages and computing environments to be included in one single notebook, provides user to document code as well as computing environment.
Proper citation: nbdocker (RRID:SCR_017159) Copy
https://knightadrc.wustl.edu/professionals-clinicians/request-center-resources/
Provides on request resources including Data: clinical and cognitive measures as well as MRI and amyloid imaging scans; Tissue: frozen brain tissue, paraffin brain sections, antemortem CSF, DNA, fibroblast, dermal fibroblasts, plasma (fasting and non-fasting) and iPSC; Participants: eligible participants may be invited to enroll in research of other investigators after appropriate review. Researchers can use the request portal to review Center guidelines and policies; view available data and tissue; access data tables and codebooks; and submit request for resources.
Proper citation: Washington University School of Medicine Knight ADRC Request Center Resources Core Facility (RRID:SCR_025254) Copy
http://montana.eagle-i.net/i/0000012b-00be-4e65-df3b-3fdc80000000
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core for Microarray analysis, Database development, Systems biology analysis, Genome assembly, Pathway data analysis, Expression data analysis, Metagenomics analysis. To maintain equipment and software for bioinformatic research, promote bioinformatics education on the MSU campus, and provide training and support to biologists implementing bioinformatics tools in their research.
Proper citation: Montana State University Bioinformatics Core Facility (RRID:SCR_009937) Copy
https://wistar.org/research-discoveries/shared-resources/bioinformatics-facility
Core provides High Throughput Data Analysis, Customized Bioinformatics Services, Custom Programming, High Performance Computing, Data management. Located in the Center for Systems and Computational Biology. Provides Cancer Center investigators with database management, software application support, expertise in statistical analyses and computational modeling of biomedical research data.
Proper citation: Wistar Bioinformatics Core Facility (RRID:SCR_010203) Copy
https://sdrc.stanford.edu/sdrc-research-cores/dctc/home/
With the following services from the Diabetes Clinical and Translational Core (DCTC), members will receive training in biospecimen preservation, study design, data analysis, data management, use of statistical software and clinical trial conduct.
Proper citation: Stanford Diabetes Research Center Diabetes Clinical and Translational Core (RRID:SCR_016212) Copy
https://sdrc.stanford.edu/sdrc-research-cores/dimc/home/
Core facility that provides immune monitoring assays at the RNA, protein, and cellular level, as well as archiving, reporting, and data mining support for clinical and translational studies related to Diabetes. The DIMC is a specialized subcore of the Human Immune Monitoring Center (HIMC) at Stanford.
Proper citation: Stanford Diabetes Research Center Diabetes Immune Monitoring Core (RRID:SCR_016210) Copy
https://voices.uchicago.edu/ucflow/
Core offers services in cytometry and antibody technology, helps to design projects, data acquisition, analysis and/or interpretation beyond routine practices,critical drafting and/or revision of manuscript for intellectual content purposes.
Proper citation: Chicago University Cytometry and Antibody Technology Core Facility (RRID:SCR_017760) Copy
Research oriented service laboratory providing informatics support to research community. Services include data analysis and mining in proteomics, genomics and chemistry, systems biology approaches such as pathway, network and interaction analyses, large scale statistical and machine learning studies, protein structure, function and stability prediction, sequence and domain analyses,d esign and implementation of relational databases and software programs, consultation on experimental design involving data acquisition, management and analysis, report, grant, and manuscript preparation.
Proper citation: Kansas University at Lawrence Applied Bioinformatics Laboratory Core Facility (RRID:SCR_017751) Copy
https://core.bioinformatics.udel.edu
CBCB Bioinformatics Data Science Core builds upon infrastructure of the Center for Bioinformatics and Computational Biology. Delaware Biotechnology Institute , Delaware Data Science Institute, and Protein Information Resource. Core helps with planning your research or analyzing your current data. Services:Consultation and Collaboration, Proposal Assistance,Training, Bioinformatics Software, Computational Hardware, Database and Web Services, Next Gen Analysis, Custom Analysis.
Proper citation: University of Delaware CBCB Bioinformatics Data Science Core Facility (RRID:SCR_017696) Copy
Resource offers range of mass spectrometry instrumentation, expertise in analysis of RNA, RNA modifications, and proteins involved in RNA metabolism/regulation, supports projects involving analysis of biomolecules, metabolites, and small synthetic molecules, provides consulting on experimental design, sample preparation and data interpretation, whole project development and grant writing contributions.
Proper citation: Albany University RNA Epitranscriptomics and Proteomics Resource Core Facility (RRID:SCR_017695) Copy
Provides evolutionary and computational biology investigators with computing and large data storage capacity for use in analyzing and managing large volumes of research data. Core contains advanced mix of high performance computing clusters, servers and data storage components, knowledge and technical skills required to compress years of analysis into days.
Proper citation: Idaho University IBEST Computational Resources Core Facility (RRID:SCR_017734) Copy
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