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https://zdock.umassmed.edu/

Web tool as protein docking server, based on rigid body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers.

Proper citation: ZDOCK Server (RRID:SCR_022518) Copy   

•   Source: SciCrunch Registry
  

https://github.com/Gaius-Augustus/learnMSA

Software tool as multiple sequence alignment formulated as statistical machine learning problem, where optimal profile hidden Markov model for potentially very large family of protein sequences is searched and alignment is decoded.

Proper citation: learnMSA (RRID:SCR_022572) Copy   

•   Source: SciCrunch Registry
  

https://github.com/FunctionLab/sei-framework

Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types.

Proper citation: sei (RRID:SCR_022571) Copy   

•   Source: SciCrunch Registry
  

https://github.com/djamesbarker/pMAT

Open source software suite for analysis of fiber photometry data.

Proper citation: pMAT (RRID:SCR_022570) Copy   

•   Source: SciCrunch Registry
  

https://github.com/JinmiaoChenLab/Rphenograph

Software R tool as simple R implementation of PhenoGraph algorithm, which is clustering method designed for high dimensional single cell data analysis.

Proper citation: Rphenograph (RRID:SCR_022603) Copy   

•   Source: SciCrunch Registry
  

https://www.ibm.com/products/structural-equation-modeling-sem

Structural equation modeling software helping support your research and theories by extending standard multivariate analysis methods, including regression, factor analysis, correlation and analysis of variance.

Proper citation: IBM SPSS Amos (RRID:SCR_022686) Copy   

•   Source: SciCrunch Registry
  

https://quality-preclinical-data.eu/about-eqipd/eqipd-quality-system/

Preclinical research quality system that can be applied in public and private sectors to ensure that early drug development research proceeds along structured lines. Used for ensuring generation of reliable preclinical data. Proposes guidance on expectations for quality related measures, defines criteria for adequate processes like performance standards, and provides examples of how such measures can be developed and implemented. EQIPD certification was established by EQIPD consortium and is now managed by its legacy organisation GoEQIPD.

Proper citation: Enhancing Quality In Preclinical Data Quality System (RRID:SCR_022729) Copy   

•   Source: SciCrunch Registry
  

https://www.rcon-ndt.com/products/radiography/x-ray-systems/phoenix-nanotom-s/

Nanofocus computed tomography system for applications in material science, precision injection moulding, micromechanics, electronics geology and biology. System includes nanofocus X-ray tube, precision mechanics and advanced software modules. Used for range of 3D CT applications., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GE: Phoenix Nanotom S system (RRID:SCR_022582) Copy   

•   Source: SciCrunch Registry
  

http://splicing.cs.washington.edu/

Web tool to predict effects of sequence variants on alternative splicing. Predicts changes in alternative 5' splice events as well as skipped exon events.

Proper citation: Hexamer Additive Linear (RRID:SCR_022581) Copy   

•   Source: SciCrunch Registry
  

https://web.rniapps.net/netshift/

Web tool for identification of driver nodes between case control association networks.Methodology for understanding driver microbes from healthy and disease microbiome datasets.

Proper citation: NetShift (RRID:SCR_022733) Copy   

•   Source: SciCrunch Registry
  

https://www.fishersci.com/shop/products/cryostar-nx50-cryostat-1/957130

Manual cryostat designed to accommodate needs of routine clinical laboratory by offering form fitting ergonomic design, with optional height adjustment, vacutome and cold D disinfection.

Proper citation: Epredia: CryoStar NX50 Cryostat (RRID:SCR_022732) Copy   

•   Source: SciCrunch Registry
  

https://upset.app/#:~:text=UpSet%20plots%20the%20intersections%20of,is%20part%20of%20an%20intersection.

Software tool to visualize set intersections in matrix layout. Interactive, web based visualization technique designed to analyze set based data. Visualizes both, set intersections and their properties, and elements in dataset. Used for quantitative analysis of data with more than three sets.

Proper citation: UpSet (RRID:SCR_022731) Copy   

•   Source: SciCrunch Registry
  

http://virtualplant.bio.nyu.edu/cgi-bin/vpweb/

Software platform to support systems biology research. Integrates genomic data and provides visualization and analysis tools for exploration of genomic data. Provides tools to generate biological hypotheses.

Proper citation: VirtualPlant (RRID:SCR_022576) Copy   

•   Source: SciCrunch Registry
  

https://www.thermofisher.com/order/catalog/product/A24811

Bentchtop Thermal Cycler for everyday PCR. Features innovative, safe heated lid and large LCD color touch screen.

Proper citation: Thermo Fisher: Applied Biosystems: SimpliAmp Thermal Cycler (RRID:SCR_023004) Copy   

•   Source: SciCrunch Registry
  

https://biccn.org/teams/u01-fischl

Project to develop and utilize imaging infrastructure to create human brain cell census and instantiate it in coordinate system that will enable immediate impact of all in vivo MRI studies of human brain. Consortium for creating cellular census of human cerebral cortex.

Proper citation: BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain (RRID:SCR_023000) Copy   

•   Source: SciCrunch Registry
  

https://www.internationalbrainlab.com/data

Data portal hosting access to behavioral data sets generated by International Brain Laboratory aiming to understand brain functions underlying decision making. Datasets are acquired in neuroscience laboratories performing experimental work. In each of these laboratories, mice are first trained in IBL decision making task following standardized training pipeline.

Proper citation: International Brain Laboratory Data (RRID:SCR_022946) Copy   

•   Source: SciCrunch Registry
  

https://pypi.org/search/?q=EmaCalc

Software package in Python for statistical analysis of Ecological Momentary Assessment data.

Proper citation: EmaCalc (RRID:SCR_022943) Copy   

•   Source: SciCrunch Registry
  

https://mriqc.readthedocs.io/en/latest/

Software tool as quality assurance workflow for Brain Imaging Data Structure compliant anatomical and functional MRI datasets. Used to extract no-reference image quality metrics from structural and functional magnetic resonance imaging data.

Proper citation: MRIQC (RRID:SCR_022942) Copy   

•   Source: SciCrunch Registry
  

https://cytotrace.stanford.edu/

Software tool that predicts differentiation state of cells from single cell RNA sequencing data. Used for predicting differentiation states from scRNA-seq data.

Proper citation: CytoTRACE (RRID:SCR_022828) Copy   

•   Source: SciCrunch Registry
  

http://www.ohsu.edu/xd/education/schools/school-of-medicine/academic-programs/neuroscience-graduate-program//

The Neuroscience Graduate Program (NGP) at OHSU provides outstanding, multidisciplinary training in neuroscience in one of the best-recognized neuroscience programs in the United States. Our graduates are distributed at top research institutions throughout the world, and the success of our faculty ensures that graduates have ready access to their next step ����?? be it postdoctoral fellowships in academia or industry, or other science-related careers. The program is particularly strong in cellular neuroscience, neuronal signaling, gene regulation, biophysics of channels and transporters, sensory systems, and neuroendocrinology with increasing strength in developmental neuroscience and disease-oriented neuroscience research. Faculty members are located within research institutes at OHSU including the Vollum Institute, the Oregon National Primate Research Center (ONPRC), Oregon Hearing Research Center, Jungers Center and the Center for Research on Occupational and Environmental Toxicology (CROET); as well as the basic and clinical departments in the OHSU School of Medicine. As time spent in the lab is the most important component of graduate science training, our program is designed such that core coursework is completed in the first year. During that first year, students also are immersed in research through lab rotations in several labs, eventually choosing one that gives a mutual fit. Because of the relatively small number of students compared to the number of neuroscience laboratories at OHSU, students have many options for a thesis lab. Our well funded faculty provide state-of-the-art exposure to the concepts and technology of modern neuroscience. OHSU also offers certificate and degree programs, e.g. technology transfer and translational science, for advanced students in the NGP who want to broaden their career options.

Proper citation: Oregon Health and Science University Neuroscience Graduate Program (RRID:SCR_003508) Copy   

•   Source: SciCrunch Registry