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http://www.stanford.edu/group/brainsinsilicon/neurogrid.html

A specialized hardware platform that will perform cortex-scale emulations while offering software-like flexibility. With sixteen 12x14 sq-mm chips (Neurocores) assembled on a 6.5x7.5 sq-in circuit board that can model a slab of cortex with up to 16x256x256 neurons - over a million! The chips are interconnected in a binary tree by 80M spike/sec links. An on-chip RAM (in each Neurocore) and an off-chip RAM (on a daughterboard, not shown) softwire vertical and horizontcal cortical connections, respectively. It provides an affordable option for brain simulations that uses analog computation to emulate ion-channel activity and uses digital communication to softwire synaptic connections. These technologies impose different constraints, because they operate in parallel and in serial, respectively. Analog computation constrains the number of distinct ion-channel populations that can be simulatedunlike digital computation, which simply takes longer to run bigger simulations. Digital communication constrains the number of synaptic connections that can be activated per secondunlike analog communication, which simply sums additional inputs onto the same wire. Working within these constraints, Neurogrid achieves its goal of simulating multiple cortical areas in real-time by making judicious choices.

Proper citation: Neurogrid (RRID:SCR_005024) Copy   

•   Source: SciCrunch Registry

http://research.cs.wisc.edu/wham/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. High-throughput sequence alignment tool that aligns short DNA sequences (reads) to the whole human genome at a rate of over 1500 million 60bps reads per hour, which is one to two orders of magnitudes faster than the leading state-of-the-art techniques. Feature list for the current version (v 0.1.5) of WHAM: * Supports paired-end reads * Supports up to 5 errores * Supports alignments with gaps * Supports quality scores for filtering invalid alignments, and sorting valid alignments * finds ALL valid alignments * Supports multi-threading * Supports rich reporting modes * Supports SAM format output

Proper citation: WHAM (RRID:SCR_005497) Copy   

•   Source: SciCrunch Registry

http://www.nescent.org/

The National Evolutionary Synthesis Center (NESCent) is a nonprofit science center dedicated to cross-disciplinary research in evolution. NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries. Synthetic research in evolutionary science takes many forms but includes integrating novel data sets and models to address important problems within a discipline, developing new analytical approaches and tools, and combining methods and perspectives from multiple disciplines to answer and even create new fundamental scientific questions. NESCent facilitates such synthetic research by providing an environment for fertile interactions among scientists. Our Science and Synthesis program sponsors postdoctoral fellows and sabbatical scholars as resident scientists, and two kinds of meetings, working groups and catalysis meetings. Catalysis meetings provide a novel mechanism for bringing together diverse research communities and cultures to identify common interests, while working groups provide an opportunity for scientists to work together intensively on fundamental synthetic questions over a several-year period. These activities are community driven through our application process and evaluated by an external advisory board. Our Informatics program provides state of the art informatics tools to visiting and in-house scientists and aims to take the lead in assembling novel databases and developing new analytical tools for evolutionary biology. Finally it is sponsoring a major initiative to provide a digital data repository for work in evolutionary biology. NESCent''s Education and Outreach group communicates the results of evolutionary biology research to the general public and scientific community, provides outreach to groups who are underrepresented in evolutionary biology and works to improve evolution education.

Proper citation: NESCent - National Evolutionary Synthesis Center (RRID:SCR_005911) Copy   

•   Source: SciCrunch Registry

http://rankprop.gs.washington.edu/svm-fold/

This web server makes predictions of family, superfamily and fold level classifications of proteins based on the Structural Classification of Proteins (SCOP) hierarchy using the Support Vector Machine (SVM) learning algorithm. SVM-FOLD detects subtle protein sequence similarities by learning from all available annotated proteins, as well as utilizing potential hits as identified by PSI-BLAST. Predictions of classes of proteins that do not have any known example with a significant pairwise PSI-BLAST E-value can still be found using SVMs.

Proper citation: SVM-fold: Protein Fold Prediction (RRID:SCR_006834) Copy   

•   Source: SciCrunch Registry

http://www.softpedia.com/get/Science-CAD/DynGO.shtml

DynGO is a client-server application that provides several advanced functionalities in addition to the standard browsing capability. DynGO allows users to conduct batch retrieval of GO annotations for a list of genes and gene products, and semantic retrieval of genes and gene products sharing similar GO annotations (which requires more disk and memory to handle the semantic retrieval). The result are shown in an association tree organized according to GO hierarchies and supported with many dynamic display options such as sorting tree nodes or changing orientation of the tree. For GO curators and frequent GO users, DynGO provides fast and convenient access to GO annotation data. DynGO is generally applicable to any data set where the records are annotated with GO terms, as illustrated by two examples. Requirements: Java Platform: Windows compatible, Linux compatible, Unix compatible

Proper citation: DynGO (RRID:SCR_007009) Copy   

•   Source: SciCrunch Registry

http://animatlab.com/

A software tool that combines biomechanical simulation and biologically realistic neural networks to create realistic models of, and perform tests on, biomechanical workings. AnimatLab was primarily designed to model and test the operation of neural circuits that might produce behavior patterns observed in an intact animal. Users can create an animalistic or robotic body and place it in a virtual environment with physics that are accurate and realistic. Users can then design a nervous system that controls the behavior of the body within the physically realistic environment. Various models for different types of actions, builds, and movements are available.

Proper citation: AnimatLab (RRID:SCR_014252) Copy   

•   Source: SciCrunch Registry

http://fatcat.burnham.org/

Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FATCAT (RRID:SCR_014631) Copy   

•   Source: SciCrunch Registry

http://www.internano.org/

Database and knowledge base of techniques for processing nanoscale materials, devices, and structures that includes step-by-step descriptions, images, notes on methodology and environmental variables, and associated references and patent information. The purpose of the Process Database is to facilitate the sharing of appropriate process knowledge across laboratories.The processes included here have been previously published or patented

Proper citation: InterNano Process Database (RRID:SCR_013719) Copy   

•   Source: SciCrunch Registry

http://www.poissonboltzmann.org/apbs/

APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. It also provides implicit solvent models of nonpolar solvation which accurately account for both repulsive and attractive solute-solvent interactions. APBS uses FEtk (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FEtk is a portable collection of finite element modeling class libraries written in an object-oriented version of C. It is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods.

Proper citation: Adaptive Poisson-Boltzmann Solver (RRID:SCR_008387) Copy   

•   Source: SciCrunch Registry

http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Jackal

Jackal is a collection of programs designed for the modeling and analysis of protein structures. Its core program is a versatile homology modeling package. It contains twelve individual programs, each with their own function.

Proper citation: Jackal (RRID:SCR_008665) Copy   

•   Source: SciCrunch Registry

http://iubio.bio.indiana.edu:8089/

Provides summary of gene and genomic information from eukaryotic organism databases. This includes gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information, links to extended gene information.

Proper citation: Eukaryote Genes (RRID:SCR_008617) Copy   

•   Source: SciCrunch Registry

https://brains.anatomy.msu.edu/brains/sheep/index.html

Online portal and image database of coronal sections of the sheep brain. Each image contains stained sections of cell bodies and myelinated fibers; nuclei and tracts are labeled.

Proper citation: Sheep Brain Atlas (RRID:SCR_001752) Copy   

•   Source: SciCrunch Registry

http://workspace.earthcube.org/cinergi

A project constructing a community inventory and knowledge base on geoscience information resources to meet the challenge of finding resources across disciplines, assessing their fitness for use in specific research scenarios, and providing tools for integrating and re-using data from multiple domains. The project team envisions a comprehensive system linking geoscience resources, users, publications, usage information, and cyberinfrastructure components. This system would serve geoscientists across all domains to efficiently use existing and emerging resources for productive and transformative research.

Proper citation: CINERGI (RRID:SCR_002188) Copy   

•   Source: SciCrunch Registry

http://research.amnh.org/atol/files/

Project whose aim is to produce a robust phylogeny of all the deepest branches within a mega-diverse group, the spiders, by combining a massive amount of newly generated comparative genomic data with a substantial set of new and re-assessed data on morphology and behavior. They propose to collect a huge amount of genomic information in order to test and improve the results achieved by over 50 detailed morphological cladistic analyses conducted by more than 30 investigators during the past 15 years. The insignificant amount of genomic work to date on spiders has been uncoordinated and of little utility for broad-scale phylogenetic investigation. The advent of high-throughput DNA sequencing, however, makes it feasible to examine substantial parts of the genome across a dense sampling of spider taxa. They propose to sequence at least 50 loci (genome samples of 500-1,000 or more base pairs that can be sequenced as single pieces in both directions simultaneously) for representatives of at least 500 genera of spiders and their closest relatives (the whipscorpion orders Amblypygi, Uropygi, and Schizomida). These genera will be carefully selected by a sampling strategy designed to maximize the resolution of deep branches within spider phylogeny, and will purposefully include all the previously most-favored study organisms of ethologists, ecologists, physiologists, and developmental and molecular biologists, thus integrating and contextualizing their research. Data matrices will be produced that combine the new genomic data with a new, comprehensive survey of morphological and behavioral homologies, offering a unique index to all comparative data on one large group. New computer software, designed in large part by members of their group and using massively parallel processing to achieve supercomputing capability, makes such analyses feasible.

Proper citation: Tree of Life: Phylogeny of Spiders (RRID:SCR_003801) Copy   

•   Source: SciCrunch Registry

http://phenoscape.org/

Project to create a scalable infrastructure that enables linking phenotypes across different fields of biology by the semantic similarity of their descriptions.

Proper citation: Phenoscape (RRID:SCR_003799) Copy   

•   Source: SciCrunch Registry

https://prr.osu.edu/

National facility for permanent curatorial preservation of rock collections from Antarctica and Southern Ocean. Repository preserves existing rock/dredge/unconsolidated/terrestrial core/photo archive collections for research use. Database allows online requests for sample loans. Mapping tool combines existing PRR database with high resolution satellite images of Antarctica, REMA or USGS topographic layers. PRR created Polar Rock Boxes for educators who are teaching about Earth science and Antarctica. Each Polar Rock Box contains samples with binder full of teaching information about Earth science and Antarctica. These boxes are freely available as short loans to US schools.

Proper citation: Polar Rock Repository (RRID:SCR_002212) Copy   

•   Source: SciCrunch Registry

https://rmats.sourceforge.io

Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P-value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user-defined threshold. From RNA-Seq data can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.

Proper citation: rMATS (RRID:SCR_023485) Copy   

•   Source: SciCrunch Registry

https://github.com/wlloyduw/ContainerProfiler

Software tool supports profiling resource utilization including CPU, memory, disk, and network metrics of containerized tasks. Resource utilization metrics are obtained across three levels: virtual machine (VM)/host, container, and process. Implementation leverages facilities provided by Linux operating system that is integral with Docker containers.

Proper citation: ContainerProfiler (RRID:SCR_023770) Copy   

•   Source: SciCrunch Registry

https://github.com/KarrLab/de_sim

Software object oriented discrete event simulation tool for complex, data driven modeling. Open source, Python based object oriented discrete event simulation tool that makes it easy to use large, heterogeneous datasets and high level data science tools such as NumPy, Scipy, pandas, and SQLAlchemy to build and simulate complex computational models.

Proper citation: DE-Sim (RRID:SCR_018770) Copy   

•   Source: SciCrunch Registry

https://github.com/PetaVision/OpenPV

Open source software neural simulation toolbox. C++ library for designing and deploying large scale neurally inspired computational models. Object oriented neural simulation toolbox optimized for high performance multi core, multi node computer architectures.

Proper citation: PetaVision (RRID:SCR_017451) Copy   

•   Source: SciCrunch Registry