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https://neurowiki.case.edu/

Curriculum materials for an Introduction to Neurobiology course for undergraduate and graduate students.

The course focuses on the analysis of neurons and neural circuits for behavior using the fundamental principles of neuroscience. From the online course syllabus, the 24 units that make up the course may be directly accessed. Each unit contains a reading, links to at least one simulation, and a problem set.

A list of all available simulations can be found here: https://neurowiki.case.edu/wiki/Simulations. * 25 simulations are written in JavaScript and will run in any browser.
Source code: https://github.com/CWRUChielLab/JSNeuroSim * Pre-compiled executables (Windows, Mac, Linux) are available for 1 desktop simulation, the Nernst Potential Simulator.
Source code: https://github.com/CWRUChielLab/Nernst Structure of the Course * Solving problems based on simulations of neuronal components, neurons, and simple circuits to understand how they work. * For advanced students, writing a neuroscience Wikipedia article, critical review, or grant, in stages.

Proper citation: NeuroWiki (RRID:SCR_004066) Copy   

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http://www.ebi.ac.uk/pdbe/

The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules.

Proper citation: PDBe - Protein Data Bank in Europe (RRID:SCR_004312) Copy   

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http://www.mprc.umaryland.edu/mbc.asp

The Maryland Brain Collection (MBC), a resource of the Maryland Psychiatric Research Center (MPRC), is dedicated to promoting research with brain tissue obtained post-mortem from individuals with schizophrenia or related disorders. The primary goal of the MBC is to provide high-quality tissue, along with comprehensive clinical information, for hypothesis-driven research. The MBC is not conceptualized as a Brain Bank with open access but is maintained and funded through collaborative research. The Maryland Brain Collection is managed by researchers at the Maryland Psychiatric Research Center (MPRC). MPRC scientists are dedicated to understanding the causes and improving the treatment of mental illness. The Maryland Brain Collection is associated with the Office of the Chief Medical Examiner for the State of Maryland and other donor sources. MPRC scientists collaborate with scientists from around the world to understand how abnormalities in brain tissue relate to mental illness. The purpose of the MBC is to study the following: Schizophrenia, Bipolar Disorder, Depression, Suicide/Teen suicide, Substance Abuse.

Proper citation: Maryland Brain Collection (RRID:SCR_004384) Copy   

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http://rarediseasesnetwork.epi.usf.edu/index.htm

The Rare Diseases Clinical Research Network (RDCRN) was created to facilitate collaboration among experts in many different types of rare diseases. Our goal is to contribute to the research and treatment of rare diseases by working together to identify biomarkers for disease risk, disease severity and activity, and clinical outcome, while also encouraging development of new approaches to diagnosis, prevention, and treatment. The Rare Diseases Clinical Research Network (RDCRN) is made up of 19 distinctive consortia that are working in concert to improve availability of rare disease information, treatment, clinical studies, and general awareness for both patients and the medical community. The RDCRN also aims to provide up-to-date information for patients and to assist in connecting patients with advocacy groups, expert doctors, and clinical research opportunities.

Proper citation: Rare Diseases Clinical Research Network (RRID:SCR_004372) Copy   

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http://www.usidnet.org/

Research consortium to advance scientific research in the primary immune deficiency diseases (PIDD) and: * Assemble and maintain a registry of patients with primary immunodeficiency diseases to provide a minimum estimate of the prevalence of each disorder in the United States. Provide a comprehensive clinical picture of each disorder and act as a resource for clinical and laboratory research. * Establish a multifaceted mentoring program to introduce new investigators into the field and stimulate interest and research in primary immune deficiency diseases. * Establish an advisory/review committee to maintain a cell/DNA Repository of biologic material from well-characterized PIDD patients for the advancement of scientific research USIDNET operates a large database of patient information for your use. The purpose and scope of this project is to assemble and maintain a registry of residents with primary immunodeficiency diseases. The project was started with the Registry of U.S. Residents with Chronic Granulomatous Disease. Since then, the registry has been expanded and now collects data on all primary immunodeficiency disorders. The following are just a few of the diseases housed in the registry: Chronic Granulomatous Disease, Common Variable Immunodeficiency Disease, DiGeorge Anomaly, Hyper IgM Syndrome, Leukocyte Adhesion Defect, Severe Combined Immunodeficiency Disease, Wiskott-Aldrich Syndrome, X-Linked Agammaglobulinemia Physicians who would like to register their patients or access the registry are encouraged to contact Onika Davis or Lamar Hamilton, USIDNET team, at odavis (at) primaryimmune.org, or lhamilton (at) primaryimmune.org

Proper citation: USIDNET: US Immunodeficiency Network (RRID:SCR_004672) Copy   

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http://em.emory.edu/protect/index.cfm

Recently, our team completed an NINDS-funded, Phase IIa double-blinded, placebo-controlled pilot clinical trial that examined the pharmacokinetics, safety, and activity of progesterone, a steroid found to have powerful neuroprotective effects in multiple animal models of brain injury. Our pilot study demonstrated a 50% reduction in death among severe TBI patients and less disability among moderate TBI patients treated with progesterone. Based on these promising results and supportive preclinical data, we are conducting a large, phase III clinical trial (ProTECT III) to definitively assess the safety and efficacy of this treatment for adults with moderate to severe acute TBI. The study is slated to begin August 2008. WHY Progesterone: Although progresterone is widely considered a sex steroid, it is also a potent neurosteroid. Progesterone is naturally synthesized in the CNS. A large and growing body of animal studies indicate that early administration of progesterone after TBI reduces cerebral edema, neuronal loss, and behavioral deficits in laboratory animals. Certain properties of progesterone make it an ideal therapeutic candidate. First, in contrast to most drugs tested to date, progesterone rapidly enters the brain and reaches equilibrium with the plasma within an hour of administration. Second, unlike other experimental agents, progesterone has a long history of safe use in humans. Finally, the findings of our pilot clinical trial (presented in the Preliminary Data Section, below) indicate that progesterone has consistent and predictable pharmacokinetic properties, is unlikely to produce harm, and may be efficacious for treating acute TBI in humans.

Proper citation: ProTECT (RRID:SCR_004531) Copy   

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http://krasnow1.gmu.edu/cn3/hippocampus3d/

Data files for a high resolution three dimensional (3D) structure of the rat hippocampus reconstructed from histological sections. The data files (supplementary data for Ropireddy et al., Neurosci., 2012 Mar 15;205:91-111) are being shared on the Windows Live cloud space provided by Microsoft. Downloadable data files include the Nissl histological images, the hippocampus layer tracings that can be visualized alone or superimposed to the corresponding Nissl images, the voxel database coordinates, and the surface rendering VRML files. * Hippocampus Nissl Images: The high resolution histological Nissl images obtained at 16 micrometer inter-slice distance for the Long-Evans rat hippocampus can be downloaded or directly viewed in a browser. This dataset consists of 230 jpeg images that cover the hippocampus from rostral to caudal poles. This image dataset is uploaded in seven parts as rar files. * Hippocampus Layer Tracings: The seven hippocampus layers ''ML, ''GC'', ''HILUS'' in DG and ''LM'', ''RAD'', ''PC'', ''OR'' in CA were segmented (traced) using the Reconstruct tool which can be downloaded from Synapse web. This tool outputs all the tracings for each image in XML format. The XML tracing files for all these seven layers for each of the above Nissl images are zipped into one file and can be downloaded. * Hippocampus VoxelDB: The 3D hippocampus reconstructed is volumetrically transformed into 16 micrometer sized voxels for all the seven layers. Each voxel is reported according to multiple coordinate systems, namely in Cartesian, along the natural hippocampal dimensions, and in reference to the canonical brain planes. The voxel database file is created in ascii format. The single voxel database file was split into three rar archive files. Please note that the three rar archive files should be downloaded and decompressed in a single directory in order to obtain the single voxel data file (Hippocampus-VoxelDB.txt). * 3D Surface Renderings: This is a rar archive file with a single VRML file containing the surface rendering of DG and CA layers. This VRML file can be opened and visualized in any VRML viewer, e.g. the open source software view3dscene. * 3D Hippocampus Movie: This movie contains visualization of the 3D surface renderings of CA (blue) and DG (red) inner and outer boundaries; neuronal embeddings of DG granule and CA pyramidal dendritic arbors; potential synapses between CA3b interneuron axon and pyramidal dendrite, and between CA2 pyramidal axon and CA pyramidal dendrites.

Proper citation: Hippocampus 3D Model (RRID:SCR_005083) Copy   

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http://www.webarraydb.org/webarray/index.html

An open source integrated microarray database and analysis suite that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion. It allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student's t-test, moderated t-tests, non-parametric tests and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters.

Proper citation: WebArrayDB (RRID:SCR_005577) Copy   

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http://www.chori.org/

CHORI is the internationally renowned biomedical research institute of Children''s Hospital and Research Center at Oakland. With world-class scientists and research centers known both nationally and internationally in multiple fields, CHORI is 5th in the nation for National Institutes of Health pediatric research funding. Bridging basic science and clinical research in the treatment and prevention of human disease, CHORI is a leader in translational research, providing cures for blood diseases, developing new vaccines for infectious diseases, and discovering new treatment protocols for previously fatal or debilitating conditions. Striving to provide the highest standard of excellence and innovation, CHORI brings together a multidisciplinary collaborative of distinguished investigators in six different Centers of Research: The Center for Cancer Research, The Center for Genetics, The Center for Immunobiology & Vaccine Development, The Center for Nutrition & Metabolism, The Center for Prevention of Obesity, Cardiovascular Disease & Diabetes, and The Center for Sickle Cell Disease & Thalassemia. Within these major areas of focus, CHORI pushes the frontiers of science and of excellence beyond their borders. Among the leading biotech enterprises in the Bay Area, CHORI produced 25 patents in the last 5 years alone. In addition to providing world-class research, CHORI is also a teaching institute, offering unique educational opportunities to high school, college, doctoral and post-doctoral students.

Proper citation: Childrens Hospital Oakland Research Institute (RRID:SCR_005582) Copy   

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http://cs.nyu.edu/~bingsun/

NYU Bioinformatics group applies algorithmic, statistical, and mathematical techniques to solve problems of interest to biology, biotechnology and biomedicine. The group focuses on bioinformatics, computational biology and systems biology with many active projects in areas ranging from single molecules to entire populations: Analysis of Single-Molecule/Single-Cell Data, SPM-based Transcriptomic Profiling, Whole-Genome Haplotype Sequencing using SMASH (Single Molecule Approaches to Haplotype Sequencing), SUTTA (Scoring and Unfolding Trimmed Tree Assembler) assembly algorithm, Analysis of Spatio-Temporal Data, Model Checking and Model Building for Systems Biology, GOALIE-based Phenomenological Models and their Verification, Causality Analysis, Causal Models and their Verification, Analysis of EHR (Electronic Health Record Data) and Disease Models (e.g., Chronic Fatigue Syndrome, Congestive Heart Failure, Deep Vein Thrombosis, etc.), Models of Cancer, Applications to Pancreatic Cancer, Polymorphisms and Biomarkers, Strategies for Group Testing, Epidemiological and Bio-Warfare Models, Planning with Large Agent Networks against Catastrophes (PLAN C), Population Genomics, and Genome Wide Association Studies (GWAS). The group has received its funding from Air Force, Army, CCPR, DARPA, NIH, NIST, NSF, NYSTAR, etc. and various other governmental and commercial entities. Currently, the group is part of an NSF funded Expedition in Computing project (CMACS: Center for Modeling and Analysis of Complex Systems at CMU) and collaborates widely, both nationally and internationally. The group is highly multi-disciplinary, attracting researchers and students from mathematics, statistics, computer science, and biology who team up with physicians, physicists, and chemists as well as professionals in their own disciplines. This group is led by Prof. Bud Mishra, a professor of computer science and mathematics at NYU''s Courant Institute of Mathematical Sciences.

Proper citation: NYU Bioinformatics Group (RRID:SCR_005697) Copy   

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http://videocast.nih.gov/

VideoCasting of special NIH events, seminars, conferences, meetings and lectures available to viewers on the NIH network and the Internet from the VideoCast web site. VideoCasting is the method of electronically streaming digitally encoded video and audio data from a server to a client. VideoCast is often referred to as streaming video. Streaming files are not downloaded, but rather are broadcast in a manner similar to television broadcasts. The videos are processed by a compression program into a streaming format and delivered in a staggered fashion to minimize impact upon the network and maximize the experience of the content for the viewer. When users request a streaming file they will receive an initial burst of data after a short delay (file latency). While content is being viewed, the streaming server machine and software continues to stream data in such a manner that the viewer experiences no break in the content. CIT can broadcast your seminar, conference or meeting live to a world-wide audience over the Internet as a real-time streaming video. The event can be recorded and made available for viewers to watch at their convenience as an on-demand video or a downloadable podcast. CIT can also broadcast NIH-only or HHS-only content.

Proper citation: NIH VideoCasting (RRID:SCR_001885) Copy   

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http://tvmouse.compmed.ucdavis.edu/

Educational resource to introduce users to the anatomy, physiology, histology, and pathology of the laboratory mouse, with an emphasis on the Genetically Engineered Mouse (GEM). It provides access to histological images, scanned at high resolution and browsable through Zoomify, movie loops and animations derived from MRI, correlated MRI and histology. It has CNS data but is focused on the whole body, e.g., physiological data is available for the heart in the form of wave patterns, histology, CNS, pathology, magnetic resonance imaging, neoplasms; animation, virtual histology, mouse, correlated imaging, necropsy, whole mouse. It may be useful to neuroscientists by relating brain anatomy to the rest of the body. There is a movie illustrating necropsy of the mouse. A link to a compendium of histological slices of brain neoplasms is provided under the Image Archive link. There is a CNS link under construction for anatomical system, which presumably will include detailed CT imaging. This site still appears to be under construction.

Proper citation: Visible Mouse Project (RRID:SCR_002393) Copy   

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http://clinicaltrials.gov/

Registry and results database of federally and privately supported clinical trials conducted in United States and around world. Provides information about purpose of trial, who may participate, locations, and phone numbers for more details. This information should be used in conjunction with advice from health care professionals.Offers information for locating federally and privately supported clinical trials for wide range of diseases and conditions. Research study in human volunteers to answer specific health questions. Interventional trials determine whether experimental treatments or new ways of using known therapies are safe and effective under controlled environments. Observational trials address health issues in large groups of people or populations in natural settings. ClinicalTrials.gov contains trials sponsored by National Institutes of Health, other federal agencies, and private industry. Studies listed in database are conducted in all 50 States and in 178 countries.

Proper citation: ClinicalTrials.gov (RRID:SCR_002309) Copy   

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http://provean.jcvi.org/

A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.

Proper citation: PROVEAN (RRID:SCR_002182) Copy   

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https://simtk.org

A National NIH Center for Biomedical Computing that focuses on physics-based simulation of biological structures and provides open access to high quality simulation tools, accurate models and the people behind them. It serves as a repository for models that are published (as well as the associated code) to create a living archive of simulation scholarship. Simtk.org is organized into projects. A project represents a research endeavor, a software package or a collection of documents and publications. Includes sharing of image files, media, references to publications and manuscripts, as well as executables and applications for download and source code. Simulation tools are free to download and space is available for developers to manage, share and disseminate code.

Proper citation: Simtk.org (RRID:SCR_002680) Copy   

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https://simtk.org/home/foldvillin

An archive of hundreds of all-atom, explicit solvent molecular dynamics simulations that were performed on a set of nine unfolded conformations of a variant of the villin headpiece subdomain (HP-35 NleNle). It includes scripts for accessing the archive of villin trajectories as well as a VMD plug-in for viewing the trajectories. In addition, all starting structures used in the trajectories are also provided. The simulations were generated using a distributed computing method utilizing the symmetric multiprocessing paradigm for individual nodes of the Folding_at_home distributed computing network. The villin trajectories in the archive are divided into two projects: PROJ3036 and PROJ3037. PROJ3036 contains trajectories starting from nine non-folded configurations. PROJ3037 contains trajectories starting from the native (folded) state. Runs 0 through 8 (in PROJ3036) correspond to starting configurations 0 through 8 discussed in the paper in J. Mol. Biol. (2007) 374(3):806-816 (see the publications tab for a full reference), whereas RUN9 uses the same starting configuration as RUN8. Each run contains 100 trajectories (named clone 0-99), each with the same starting configuration but different random velocities. Trajectories vary in their length of time and are subdivided into frames, also known as a generation. Each frame contains around 400 configurational snapshots, or timepoints, of the trajectory, with the last configurational snapshot of frame i corresponding to the first configurational snapshot of generation i+1. The goal is to allow researchers to analyze and benefit from the many trajectories produced through the simulations.

Proper citation: Molecular Simulation Trajectories Archive of a Villin Variant (RRID:SCR_002704) Copy   

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http://mialab.mrn.org/software/eegift/index.html

Implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) EEG data. This MATLAB toolbox is compatible with MATLAB 6.5 and higher.

Proper citation: Group ICA Of EEG Toolbox (RRID:SCR_002478) Copy   

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https://dpcpsi.nih.gov/onr/nrcc

Coordinates nutritional sciences-related research and research training across the National Institutes of Health (NIH) and among Federal Agencies by providing mechanisms to communicate research, research training, policy, and education initiatives. The DNRC facilitates the exchange of information, coordinates workshops and seminars on critical issues, encourages national and international research collaborations, and serves as the NIH primary point of contact for the Department of Health and Human Services (DHHS) and other agencies, departments, and organizations in matters pertaining to nutritional sciences and physical activity. Through its dedicated efforts to promote scientific policy reviews, innovative research, interagency collaboration, and technical advancements, the DNRC strives to define the increasing roles of nutritional sciences and physical activity in health promotion and disease prevention and treatment.

Proper citation: NIH Division of Nutrition Research Coordination (RRID:SCR_001469) Copy   

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http://nashua.case.edu/PathwaysWeb/Web/

An integrated software system for storing, managing, analyzing, and querying biological pathways at different levels of genetic, molecular, biochemical and organismal detail. The system contains a pathways database and associated tools to store, compare, query, and visualize metabolic pathways. The aim is to develop an integrated database and the associated tools to support computational analysis and visualization of biochemical pathways. At the computational level, PathCase allows users to visualize pathways in multiple abstraction levels, and to pose predetermined and ad hoc queries using a graphical user interface. Pathways are represented as graphs, and implemented as a relational database. The available functional annotations include the identity of the substrate(s), product(s), cofactors, activators, inhibitors, enzymes or other processing molecules, GO-categories of enzymes (as well as GO hierarchy visualizations two-way-linked to PathCase enzymes), EC number information and the associated links, and synonyms and encoding genes of gene products.

Proper citation: PathCase Pathways Database System (RRID:SCR_001835) Copy   

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https://bioinformaticshome.com/tools/rna-seq/descriptions/LIGER.html

Software R package for integrating and analyzing multiple single-cell datasets. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors. Used for analysis of multiple scRNA-seq data sets.

Proper citation: LIGER (RRID:SCR_018100) Copy   

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