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https://github.com/walaj/svaba
Software tool for detecting structural variants in sequencing data using genome wide local assembly. Genome wide detection of structural variants and indels by local assembly. Used for detecting SVs from short read sequencing data using genome wide local assembly with low memory and computing requirements.
Proper citation: SvABA (RRID:SCR_022998) Copy
http://www.brainhealthdatabank.ca
Repository of many types and sources of data including, but not limited to, assessments, imaging, wearable, and biological samples, collected from research projects at the Centre for Addiction and Mental Health. Data that individuals choose to share to advance mental health.
Proper citation: BrainHealth Databank (RRID:SCR_022996) Copy
Organization to optimize the care of women, men, and children with lower urinary tract dysfunction and/or pelvic floor disorders through education, research and involvement in health care policy. To improve the art and science of Urology through basic and applied clinical research in urodynamics and neurourology, voiding function and dysfunction, female urology and pelvic floor dysfunction, and to disseminate and teach these concepts.
Proper citation: Society of Urodynamics, Female Pelvic Medicine and Urogenital Reconstruction (SUFU) (RRID:SCR_022874) Copy
Research and education program in Harvard Program in Therapeutic Science at Harvard Medical School to advance science and to develop technology needed to accelerate invention of new medicines and personalization of patient care. Used to study molecular causes of disease, ways drugs exert their therapeutic and adverse effects, design and interpretation of clinical trials.
Proper citation: Laboratory of Systems Pharmacology program (RRID:SCR_022873) Copy
https://www.pinnaclet.com/sleepPRO.html
Software tool to reduce scoring time and simplify data analysis. Offers automated power analysis, semi-automated scoring methods, and advanced tabular and graphical analysis for investigating sleep data sets. Custom scoring and analysis are also available. Scoring sessions between two or more users can be compared. All EEG/EMG and video data sets recorded with Pinnacle software, as well as third party EDF files, can be imported.
Proper citation: Sirenia Sleep Pro (RRID:SCR_022918) Copy
https://www.genoscope.cns.fr/brassicanapus/
Web tool as Brassica napus genome browser.
Proper citation: CNS Genoscope (RRID:SCR_023020) Copy
https://github.com/c-zhou/yahs
Software command line tool for construction of chromosome scale scaffolds from Hi-C data. Scaffolding tool using Hi-C or Omni-C data. Used to scaffold contig level assemblies into chromosome scale scaffolded assemblies.
Proper citation: YaHS (RRID:SCR_022965) Copy
https://www.iveindhoven.com/en/article/reichert-jung-ultracut-e-ultramicrotome/
Reichert Jung Ultracut E, article number 131-960, is used to cut ultrathin and semithin sections of resin embedded samples for electron microscopy.
Proper citation: Ultracut: E ultramicrotome (RRID:SCR_022980) Copy
Software suite to analyse gait trials collected with Experimental Dynamic Gait Arena for Rodents. Used for rodent gait analysis.
Proper citation: GAITOR Suite (RRID:SCR_023031) Copy
The Precellys 24 homogenizer with automatic tube locking system with the ability to process up to 24 tubes simultaneously., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Bertin Technologies: Precellys 24 tissue homogenizer (RRID:SCR_022979) Copy
https://www.emkatech.com/product/iox2-software/
Software tool to acquire, analyze, view, and store physiological data generated during preclinical experiment. Has library of application specific analysis modules for real time signal processing.
Proper citation: IOX2 (RRID:SCR_022973) Copy
https://www.inscopix.com/nvoke
Miniature microscope system that integrates in vivo cellular resolution calcium imaging with simultaneous or sequential optogenetic manipulation to causally link neural circuit activity with behavior.
Proper citation: iNSCOPIX: nVoke System (RRID:SCR_023028) Copy
https://open-brain-consent.readthedocs.io/en/stable/
Platform for informing research participants and obtaining consent to share brain imaging data. Provides suggested wording/templates for MRI studies human participant consent forms (including GDPR version), reference of tools for data anonymization, etc to make prospective data sharing possible.
Proper citation: Open Brain Consent (RRID:SCR_022972) Copy
https://labsyspharm.github.io/jekyll-tutorial/
Website tutorial for creating Jekyll-based scientific website, including editing in GitHub, working locally with Jekyll and applying Jekyll and Markdown formatting basics, and using custom themes.
Proper citation: Jekyll Tutorial (RRID:SCR_022859) Copy
http://exon.cshl.org/cgi-bin/atprobe/atprobe.pl
Arabidopsis thaliana promoter binding element database that focuses on specific binding elements on known genes, found with experimental methods.
Proper citation: AtProbe (RRID:SCR_005412) Copy
http://cgi-www.daimi.au.dk/cgi-chili/datfap/frontdoor.py
A database of transcription factors from 13 plant species, and PCR primers for around 90% of them.
Proper citation: DATFAP (RRID:SCR_005413) Copy
http://bioinfozen.uncc.edu/tfindit/
A database and web service for structural bioinformatics studies of transcription factor (TF)-DNA interactions. Various datasets can be generated based on one or more search options specified by users.
Proper citation: TFinDIT (RRID:SCR_005411) Copy
Database for identifying orthologous phenotypes (phenologs). Mapping between genotype and phenotype is often non-obvious, complicating prediction of genes underlying specific phenotypes. This problem can be addressed through comparative analyses of phenotypes. We define phenologs based upon overlapping sets of orthologous genes associated with each phenotype. Comparisons of >189,000 human, mouse, yeast, and worm gene-phenotype associations reveal many significant phenologs, including novel non-obvious human disease models. For example, phenologs suggest a yeast model for mammalian angiogenesis defects and an invertebrate model for vertebrate neural tube birth defects. Phenologs thus create a rich framework for comparing mutational phenotypes, identify adaptive reuse of gene systems, and suggest new disease genes. To search for phenologs, go to the basic search page and enter a list of genes in the box provided, using Entrez gene identifiers for mouse/human genes, locus ids for yeast (e.g., YHR200W), or sequence names for worm (e.g., B0205.3). It is expected that this list of genes will all be associated with a particular system, trait, mutational phenotype, or disease. The search will return all identified model organism/human mutational phenotypes that show any overlap with the input set of the genes, ranked according to their hypergeometric probability scores. Clicking on a particular phenolog will result in a list of genes associated with the phenotype, from which potential new candidate genes can identified. Currently known phenotypes in the database are available from the link labeled ''Find phenotypes'', where the associated gene can be submitted as queries, or alternately, can be searched directly from the link provided.
Proper citation: Phenologs (RRID:SCR_005529) Copy
Bradley Voytek''''s blog is where he tries out new ideas. He will often be wrong, but that''''s the point. He is a Neuroscientist studying human cognition, neuroplasticity, and brain computer interfacing. Into really geeky stuff. World zombie neuroscience expert. Also runs brainSCANr.com with his wife, Jessica.
Proper citation: Oscillatory Thoughts (RRID:SCR_005481) Copy
Biospecimen repository of normal and diseased human material from a variety of tissues and conditions along with clinical annotation. Both frozen aliquots and paraffin embedded tissue are available. Biospecimens are available to qualified researchers with IRB approval. * Preliminary inquires please contact Cheryl Spencer at cheryl.spencer (at) bmc.org
Proper citation: Boston University Biospecimen Archive Research Core (RRID:SCR_005363) Copy
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