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https://github.com/mwang87/MassQueryLanguage

Software application for universal searching of Mass Spectrometry data. Open source MS query language for flexible and mass spectrometer manufacturer-independent mining of MS data. Implements common MS terminology to build consensus vocabulary to search for MS patterns in single mass spectrometry run. Enables set of mass spectrometry patterns to be queried directly from raw data.

Proper citation: MassQL (RRID:SCR_025106) Copy   

•   Source: SciCrunch Registry

http://www.uwyo.edu/buerkle/software/bamova/

Software that implements a Bayesian Analysis of Molecular Variance and different likelihood models for three different types of molecular data (including two models for high throughput sequence data).

Proper citation: bamova (RRID:SCR_000510) Copy   

•   Source: SciCrunch Registry

http://www.cs.utah.edu/~miriah/pathline/Overview.html

Software visualization tool for comparative functional genomics that supports analysis of three types of biological data at once: functional data such as gene activity measurements; pathway data that presents a series of reactions within a cellular process; and phylogenetic data describing ancestral relationships between species. The design of Pathline includes two new visual encoding techniques. The first is an encoding of a linearized metabolic pathway representation that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is a curvemap, a matrix layout of temporal expression data for enhanced perception of trends in gene and cell activity levels across multiple species.

Proper citation: Pathline (RRID:SCR_000635) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/LOVE

A versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS surfaces, atlas hierarchical brain-region labelings ( Brain Trees). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest. The 3D features of the package include a SurfaceViewer and a full real-time VolumeRenderer. These allow the user to view the relative positions of different anatomical or functional regions which are not co-planar in any of the axial, sagittal or coronal 2D projection planes. The interactive part of LONI_Viz features a region drawing module used for manual delineation of regions of interest. A series of 2D contours describing the boundary of a region in projection planes (axial, sagittal or coronal) could be used to reconstruct the surface-representation of the 3D outer shell of the region. The latter could then be resliced in directions complementary to the drawing-direction and these complementary contours could be loaded in all tree cardinal views. In addition the surface object could be displayed using the SurfaceViewer. A pre-loading data crop and sub-sampling module allows the user to load and view practically data of any size. This is especially important when viewing cryotome, histological or stained data-sets which may reach 1GB (109 bytes) in size. The user could overlay several pre-registered volumes, change intensity colors and ranges and the inter-volume opacities to visually inspect similarities and differences between the different subjects/modalities. Several image-processing aids provide histogram plotting, image-smoothing, etc. Specific Features: * Region description DataBase * Moleculo-genetic database * Brain anatomical data viewer * BrainMapper tool * Surface (LightWave objects/scenes) and Volume rendering tools * Interactive Contour Drawing tool Implementation Issues: * Applet vs. Application - the software is available as both an applet and a standalone application. The former could be used to browse data from within the LONI database, however, it imposes restrictions on file-size, Internet connection and network-bandwidth and client/server file access. The later requires a local install and configuration of the LONI_Viz software * Extendable object-oriented code (Java), computer architecture independent * Complete online software documentation is available at http://www.loni.ucla.edu/LONI_Viz and a Java-Class documentation is available at http://www.loni.ucla.edu/~dinov/LONI_Vis.dir/doc/LONI_Viz_Java_Docs.html

Proper citation: LONI Visualization Tool (RRID:SCR_000765) Copy   

•   Source: SciCrunch Registry

http://megasoftware.net/

Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny.

Proper citation: MEGA (RRID:SCR_000667) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/group/Urchin/contents.html

Laboratory modules designed for high school students covering sea urchin embryology including fertilization and development.

Proper citation: Sea Urchin Embryology (RRID:SCR_000460) Copy   

•   Source: SciCrunch Registry

http://zoobank.org/

A database of scientific names in zoology. ZooBank is an online, open-access, community-generated registry for zoological nomenclature. It serves as a service to taxonomists, biologists, and the global diversity informatics community. It is the Official Register of the International Commission on Zoological Nomenclature (ICZN).

Proper citation: ZooBank (RRID:SCR_000901) Copy   

•   Source: SciCrunch Registry

https://3dvcell.ncbi.nlm.nih.gov/

THIS RESOURCE IS NO LONGER IN SERVICE, confirmed by curator 11/21/2018; Community of researchers attempting to build a comprehensive virtual cell model. The 3DVC will do for cell biology what the Large Hadron Collider (LHC) does for particle physics, but through a virtual rather than physical resource. It will bring together collaborators around a shared infrastructure to advance the field through efficient groundbreaking science and technology, the results of which will be broadly disseminated to an audience ranging from K12 to professionals. The 3DVC is committed to open science, yet strives for sustainability through new business models that leverages that open content.

Proper citation: 3DVC (RRID:SCR_001377) Copy   

•   Source: SciCrunch Registry

http://www.archive.org/

An Internet library offering the general public access to historical collections that exist in digital format including texts, audio, moving images, and software. Additionally it provides archived web pages in their collections, and specialized services for adaptive reading and information access for the blind and other persons with disabilities. Founded in 1996 and located in San Francisco, the Archive has been receiving data donations from Alexa Internet and others. In late 1999, the organization started to grow to include more well-rounded collections.

Proper citation: Internet Archive (RRID:SCR_001682) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.plantgdb.org/AtGDB/

Database providing a sequence-centered genome view for Arabidopsis thaliana, with a narrow focus on gene structure annotation. The current genome assembly displayed at AtGDB is version TAIR9. Annotated gene models are TAIR10. They have mapped the complete set of 176,915 publicly available Arabidopsis EST sequences onto the Arabidopsis genome using GeneSeqer, a spliced alignment program incorporating sequence similarity and splice site scoring. About 96% of the available ESTs could be properly aligned with a genomic locus, with the remaining ESTs deriving from organelle genomes and non-Arabidopsis sources or displaying insufficient sequence quality for alignment. The mapping provides verified sets of EST clusters for evaluation of EST clustering programs. Analysis of the spliced alignments suggests corrections to current gene structure annotation and provides examples of alternative and non-canonical pre-mRNA splicing.

Proper citation: Arabidopsis thaliana Genome Database (RRID:SCR_001901) 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

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://www.unavco.org/

A non-profit university-governed consortium that facilitates geoscience research and education using geodesy. It rovides access to and submission of Geodetic GPS / GNSS Data, Geodetic Imaging Data, Strain and Seismic Borehole Data, and Meteorological Data. Data access web services/API provides the ability to use a command line interface to query metadata and obtain URLs to data and products. UNAVCO also provides a variety of software, including web applications, and desktop utilities for scientists, instructors, students, and others. Web-based data visualization and mapping tools provide users with the ability to view postprocessed data while web-based geodetic utilities provide ancillary information. Downloadable stand-alone software utilities include applications for configuring instruments, managing data collection, download and transfer, and performing computations on the raw data, e.g., data pre-processing or processing. The UNAVCO Facility in Boulder, Colorado is the primary operational activity of UNAVCO and exists to support university and other research investigators in their use of geophysical sensor technology for Earth sciences research. The Facility performs this task in part by archiving GNSS/GPS data and data products for current and future applications. Other data types that scientists use for Earth deformation studies are also held in the UNAVCO Archive collections. UNAVCO operates a community Archive, which provides long-term secure storage and easy retrieval of GNSS data, strain data, various derived products and related metadata. The Archive primarily stores high-precision geodetic data used for research purposes, collected under National Science Foundation and NASA sponsored projects. UNAVCO provides many learning opportunities including: Short Courses and Workshops, Educational Resources, RESESS Research Student Internships, and Technical Training.

Proper citation: UNAVCO (RRID:SCR_006706) Copy   

•   Source: SciCrunch Registry

http://media.marine-geo.org/

A collection of high-quality images and videos for education and outreach from the Integrated Earth Data Applications Facility. Albums include: Ridge2000, MARGINS, GeoMapApp, GeoPRISMS, Antarctic and Southern Ocean, Global Multi-Resolution Topography. To contribute your media to Media Bank, you are asked to supply metadata with each image/video supplied.

Proper citation: Marine Geosciences Data System MediaBank (RRID:SCR_006875) Copy   

•   Source: SciCrunch Registry

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://rankprop.gs.washington.edu/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on May,18,2020. Ranking algorithm that exploits global network structure of similarity relationships among proteins in database by performing diffusion operation on protein similarity network with weighted edges. Source code and web server for searching non-redundant protein database. Web server ranks proteins found in NRDB40 (from PairsDB) against query sequence of amino acids using Rankprop algorithm.

Proper citation: Rankprop - Protein Ranking by Network Propagation (RRID:SCR_007159) Copy   

•   Source: SciCrunch Registry