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http://bio.math.berkeley.edu/eXpress/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented January 29, 2018.
From website: "Note that the eXpress software is also no longer being developed. We recommend you use kallisto instead." Kallisto can be found at http://pachterlab.github.io/kallisto/.

Software for streaming quantification for high-throughput DNA/RNA sequencing.
Can be used in any application where abundances of target sequences need to be estimated from short reads sequenced from them.

Proper citation: eXpress (RRID:SCR_006873) Copy   

•   Source: SciCrunch Registry

http://www.compneurosci.com/CoSMo2012/

This unique summer school focuses on computational techniques integrating the multi-disciplinary nature of sensory-motor neuroscience through combined empirical-theoretical teaching modules and a focus on the use of databases of movement data (NSF CRCNS). Major breakthroughs in brain research have been achieved through computational models. The goal of the Summer School in Computational Sensory-Motor Neuroscience is to provide cross-disciplinary training in mathematical modelling techniques relevant to understanding brain function, dysfunction and treatment. In a unique approach bridging experimental research, clinical pathology and computer simulations, students will learn how to translate ideas and empirical findings into mathematical models. Students will gain a profound understanding of the brain''s working principles and diseases using advanced modelling techniques in hands-on simulations of models during tutored sessions by making use of data / model sharing. This summer school aims at propelling promising students into world-class researchers. Dates: August 5-19, 2012 Location: Northwestern University Chicago (Evanston campus), Illinois, USA Deadlines: * April 22, 2012: Application due, including letters of reference (extended!!!) * May 1, 2012: Notification of acceptance * May 20, 2012: Attendance confirmation of applicants and registration payment This summer school is directed at graduate students and post-doctoral fellows from multi-disciplinary backgrounds, including Life Sciences, Psychology, Computer Science, Mathematics and Engineering. We will also accept highly motivated outstanding under-graduate students. There are no formal prerequisites, but basic knowledge in calculus, linear algebra, neuroscience and the Matlab simulation environment is expected. Enrollment will be limited to 40 participants.

Proper citation: Summer School in Computational Sensory-Motor Neuroscience (RRID:SCR_006894) 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://neurodata.io/

Project portal dedicated to understand animal and machine intelligence and repository of data and tools. Suite of tools to analyze and graph imaging data. Image and data repository for large, publicly available neuro-specific data files and images. Contains tools for analytics, databases, cloud computing, and Web-services applied to both big neuroimages and big neurographs.

Proper citation: neurodata (RRID:SCR_014264) 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://cellorganizer.org

Image analysis software that learns modular models of things such as cell shape, nuclear shape, vesicular organelle distribution and microtubule distribution directly from 2D or 3D images and can produce specific instances of cell geometries without the need to create them by hand or to segment microscope images. These geometries can be combined with biochemical models to perform spatially realistic cell simulations if used in conjunction with MCell.

Proper citation: CellOrganizer (RRID:SCR_014828) Copy   

•   Source: SciCrunch Registry

https://elegansvariation.org/

Supplier and researcher of wild C. elegans strains. CeNDR supplies organisms, analyzes whole-genome sequences, and facilitates genetic mappings to aid researchers in gene discovery.

Proper citation: Caenorhabditis elegans Natural Diversity Resource (CeNDR) (RRID:SCR_014958) Copy   

•   Source: SciCrunch Registry

http://www.chlamycollection.org/

Central repository that receives, catalogs, preserves, and distributes wild type and mutant cultures of the green alga Chlamydomonas reinhardtii, as well as useful molecular reagents and kits for education and research.

Proper citation: Chlamydomonas Resource Center (RRID:SCR_014960) Copy   

•   Source: SciCrunch Registry

http://opm.phar.umich.edu/

Database that provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal.

Proper citation: Orientations of Proteins in Membranes database (RRID:SCR_011961) Copy   

•   Source: SciCrunch Registry

http://www.datamonkey.org/

Web-based suite of phylogenetic analysis tools for use in evolutionary biology. Web application for comparative analysis of sequence alignments using statistical models. Used for analyzing evolutionary signatures in sequence data. Datamonkey 2.0 provides curated collection of methods for interrogating coding-sequence alignments for imprints of natural selection, packaged as a responsive (i.e. can be viewed on tablet and mobile devices), fully interactive, and API-enabled web application.

Proper citation: Datamonkey (RRID:SCR_010278) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/InterNano

A custom-built terminology to describe the nanomanufacturing enterprise.

Proper citation: InterNano Nanomanufacturing Taxonomy (RRID:SCR_010346) Copy   

•   Source: SciCrunch Registry

http://www.aoncadis.org

A repository and data management services for Arctic research data. Data include long-term observational timeseries, local, regional, and system-scale research from many diverse domains.

Proper citation: ACADIS Gateway (RRID:SCR_010473) Copy   

•   Source: SciCrunch Registry

http://evolution.genetics.washington.edu/phylip/software.html

392 phylogeny software packages and 54 free web servers describing all known software for inferring phylogenies (evolutionary trees). Submissions are welcome. Programs are listed by methods available, by computer systems on which they work, cross-referenced by method and by computer system, by ones which analyze particular kinds of data, to show the most recent listings, or to show ones most recently changed.

Proper citation: Phylogeny Programs (RRID:SCR_010797) Copy   

•   Source: SciCrunch Registry

http://casp.rnet.missouri.edu/soydb/

A Knowledge Database of Soybean Transcription Factors. PSI-BLAST is available to find hits from the database.

Proper citation: SoyDB (RRID:SCR_010900) 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://wings-workflows.org

A software application which assists scientists with designing computational experiments. WINGS is a semantic workflow system which incorporates semantic constraints about datasets and workflow components into its workflow representations. The workflow system has an open modular design and can be easily integrated with other existing workflow systems and execution frameworks to extend them with semantic reasoning capabilities. WINGS also allows users to express high-level descriptions of their analysis goals, and assists them by automatically and systematically generating possible workflows that are consistent with that request. In cases where privacy or off-line use are important, WINGS can submit workflows in a scripted format for execution in the local host. It uses Pegasus or OODT as the execution engine for large-scale distributed workflow execution.

Proper citation: WINGS (RRID:SCR_013997) Copy   

•   Source: SciCrunch Registry

https://github.com/SantamariaLab/NeuroManager

Simulation submission manager for computational neuroscience. It manages simulation processing, file transfers, and job submission for a heterogeneous mixture of standalone server, cluster, and cloud servers.

Proper citation: NeuroManager (RRID:SCR_015559) Copy   

•   Source: SciCrunch Registry

https://www.rosettacommons.org/home

Molecular modeling software package for 3D structure prediction and high resolution design of proteins, nucleic acids, and non natural polymers. Used in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.

Proper citation: Rosetta (RRID:SCR_015701) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/amap-align/

Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method.

Proper citation: AMAP (RRID:SCR_015969) Copy   

•   Source: SciCrunch Registry