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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001096/

Software pipeline to identify MITEs as well as other small Class 2 non autonomous Transposable Elements from genomic DNA data sets. Used for discovering miniature inverted repeat transposable elements from genomic sequences. Can search large genomic data sets including whole genome sequences.

Proper citation: MITE-Hunter (RRID:SCR_020946) Copy   

•   Source: SciCrunch Registry

https://www.biosimulations.org/

Web tool for sharing and re-using biomodels, simulations, and visualizations of simulations results. Supports variety of modeling frameworks including kinetic, constraint based, and logical modeling, model formats including BNGL, CellML, SBML, and simulation tools including COPASI, libRoadRunner/tellurium, NFSim, VCell.

Proper citation: BioSimulations (RRID:SCR_018733) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/reprocontainers/

Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments.

Proper citation: ReproNim/containers (RRID:SCR_018467) Copy   

•   Source: SciCrunch Registry

http://clavius.bc.edu/~clotelab/DiANNA/

Neural network and web server, which determines cysteine oxidation state and disulfide connectivity of protein, given only its amino acid sequence. Used to predict disulfide connectivity topology. Predicts which half-cystines are covalently bound to which other half-cystines. DiANNA 1.1 is extension of DiANNA web server for ternary cysteine classification.

Proper citation: DiANNA (RRID:SCR_018529) Copy   

•   Source: SciCrunch Registry

https://www.bpforms.org

Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts.

Proper citation: BpForms (RRID:SCR_018653) Copy   

•   Source: SciCrunch Registry

https://www.objtables.org

Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort.

Proper citation: ObjTables (RRID:SCR_018652) Copy   

•   Source: SciCrunch Registry

https://github.com/OHDSI/CohortMethod

Software R package for performing new user cohort studies in observational database in OMOP Common Data Model.

Proper citation: CohortMethod (RRID:SCR_018511) Copy   

•   Source: SciCrunch Registry

https://rosie.graylab.jhu.edu/docking2

Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community.

Proper citation: ROSIE (RRID:SCR_018764) Copy   

•   Source: SciCrunch Registry

https://github.com/chris-mcginnis-ucsf/DoubletFinder

Software R package that predicts doublets in single cell RNA sequencing data. Doublet detection in single cell RNA sequencing data using artificial nearest neighbors. Identifies doublets using only gene expression data.

Proper citation: DoubletFinder (RRID:SCR_018771) Copy   

•   Source: SciCrunch Registry

http://qutublab.rice.edu/cytoNet/

Cloud based analysis software for cell population microscopy images. Network Analysis of Cell Communities cytoNet image analysis software designed to quantify structure of cell communities from microscope images, using principles of graph theory.

Proper citation: cytoNet (RRID:SCR_017465) Copy   

•   Source: SciCrunch Registry

https://github.com/Mark-Kramer/Seizure-Waves

Analysis and modeling code for waves of seizure activity.

Proper citation: Seizure-Waves (RRID:SCR_017455) Copy   

•   Source: SciCrunch Registry

http://compbio.mit.edu/ChromHMM/

Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations.

Proper citation: ChromHMM (RRID:SCR_018141) Copy   

•   Source: SciCrunch Registry

http://raptorx.uchicago.edu/

Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model.

Proper citation: RaptorX (RRID:SCR_018118) Copy   

•   Source: SciCrunch Registry

http://ultrascan.aucsolutions.com/

Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis.

Proper citation: UltraScan (RRID:SCR_018126) Copy   

•   Source: SciCrunch Registry

http://titan.biotec.uiuc.edu/bee/honeybee_project.htm

A database integrating data from the bee brain EST sequencing project with data from sequencing and gene research projects from other organisms, primarily the fruit fly Drosophila melanogaster. The goal of Bee-ESTdb is to provide updated information on the genes of the honey bee, currently using annotation primarily from flies to suggest cellular roles, biological functions, and evolutionary relationships. The site allows searches by sequence ID, EST annotations, Gene Ontology terms, Contig ID and using BLAST. Very nice resource for those interested in comparative genomics of brain. A normalized unidirectional cDNA library was made in the laboratory of Prof. Bento Soares, University of Iowa. The library was subsequently subtracted. Over 20,000 cDNA clones were partially sequenced from the normalized and subtracted libraries at the Keck Center, resulting in 15,311 vector-trimmed, high-quality, sequences with an average read length of 494 bp. and average base-quality of 41. These sequences were assembled into 8966 putatively unique sequences, which were tested for similarity to sequences in the public databases with a variety of BLAST searches. The Clemson University Genomics Institute is the distributor of these public domain cDNA clones. For information on how to purchase an individual clone or the entire collection, please contact www.genome.clemson.edu/orders/ or generobi (at) life.uiuc.edu.

Proper citation: Honey Bee Brain EST Project (RRID:SCR_002389) Copy   

•   Source: SciCrunch Registry

http://cgsc.biology.yale.edu/index.php

The CGSC Collection contains only non-pathogenic BSL-1 laboratory strains, primarily genetic derivatives of Escherichia coli K-12, the laboratory strain widely used in genetic and molecular studies, but a few B strains. The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. The public version of the database includes this information and can be queried directly via this CGSC DB WebServer. The collection includes cultures of wild-type contributed from a number of laboratories and a few thousand derivatives carrying one or up to 29 mutations from among 3500 mutations in (or included in deletions spanning) more than 1300 different loci. Some combinations were constructed particularly for mapping purposes and are still used for teaching and for rapid localization, some for manifestation of a particular phenotype, some strains for transferring a particular region or for complementation analysis. Some plasmids, e.g., the Clarke and Carbon collection, F-primes, a number of toolkit plasmids, and a few classic plasmids are included, but it is not a comprehensive collection of plasmids. Additionally, we have recently acquired most of the strains from the Keio Collection of systematic individual gene knockout (deletion/kan insertion) strains.

Proper citation: CGSC (RRID:SCR_002303) Copy   

•   Source: SciCrunch Registry

http://cbl.uh.edu/ORION/research/software

ORION is our neuron reconstruction software package developed for the morphological reconstruction of neurons from confocal and multiphoton microscopy data. It accepts raw neuron stack data as input and it is capable of reconstructing the neuron structure, visualizing the output, and exporting the reconstruction in a variety of formats. We are developing tools that will enable Neuroscientists to explore single neuron function via sophisticated image analysis. Advanced optical imaging can produce both structural and functional data and is at the forefront of experimentally exploring the fast, small-scale dynamics of living neurons. Further, compartmental modeling of neuronal function enables rapid testing of hypotheses and estimating experimentally inaccessible parameters. Combining these two techniques will afford unprecedented capabilities in the study of single neuron function. Our software utility bridges the two Neuroscience techniques by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function.

Proper citation: ORION Software (RRID:SCR_004389) Copy   

•   Source: SciCrunch Registry

http://www.scrible.com/#desktop

We''re bringing Web-based research into the Internet Era by empowering people to mark up web pages in the browser and manage and collaborate on them online. And that''s just the start... We''ve got much more planned in a variety of areas to help people manage the mounds of info they''re pulling off the Web everyday. Simply drag the scrible bookmarklet to your browser''s Bookmarks toolbar. Click it later to mark up, save or share web pages. Even though the world uses the Internet to research nearly everything for work, school and home (job postings, press releases, Wikipedia articles, medical info, etc.), most folks still use old-school ways of annotating, organizing and sharing online info (printing to mark by hand, copying/pasting into Word, etc.). It''s archaic, laborious and a waste of time. We''re changing that. A bookmarklet is a bookmarked link that, when clicked, adds functionality to your browser. When the scrible Bookmarklet is clicked, it loads the scrible Toolbar atop the current webpage you''re viewing. Adding the scrible Bookmarklet to your browser is a breeze. Simply drag it to your browser''s Bookmarks Toolbar.

Proper citation: scrible (RRID:SCR_008882) Copy   

•   Source: SciCrunch Registry

http://alchemy.sourceforge.net/

ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed.

Proper citation: ALCHEMY (RRID:SCR_005761) Copy   

•   Source: SciCrunch Registry

http://www.inbre.montana.edu/bioinformatics/functional_genomics/index.html

Core provides instrumentation and support for academic investigators throughout Montana and Rocky Mountain west. For most instrumentation, facility provides instruction and supervision followed by independent user access. For those doing Affymetrix microarrays, facility can also accept RNA samples and provides full service processing. Assists with experimental planning and grantmanship phases.

Proper citation: Montana State University Functional Genomics Core Facility (RRID:SCR_009939) Copy   

•   Source: SciCrunch Registry