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https://github.com/alyssafrazee/polyester

An R package designed to simulate RNA sequencing experiments with differential transcript expression. Given a set of annotated transcripts, it will simulate the steps of an RNA-seq experiment (fragmentation, reverse-complementing, and sequencing) and produce files containing simulated RNA-seq reads. Simulated reads can be analyzed using a choice of downstream analysis tools. Polyester has a built-in wrapper function to simulate a case/control experiment with differential transcript expression and biological replicates. Users are able to set the levels of differential expression at transcripts of their choosing. This means they know which transcripts are differentially expressed in the simulated dataset, so accuracy of statistical methods for differential expression detection can be analyzed. Polyester offers several unique features: * Built-in functionality to simulate differential expression at the transcript level * Ability to explicitly set differential expression signal strength * Simulation of small datasets, since large RNA-seq datasets can require lots of time and computing resources to analyze * Generation of raw RNA-seq reads, as opposed to alignments or transcript-level abundance estimates * Transparency/open-source code

Proper citation: Polyester (RRID:SCR_003602) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/simtkcore

SimTK Core is one of the two packages that together constitute SimTK, the biosimulation toolkit from the Simbios Center. The other major component of SimTK is OpenMM which is packaged separately. This SimTK Core project collects together all the binaries needed for the various SimTK Core subprojects. These include Simbody, Molmodel, Simmath (including Ipopt), Simmatrix, CPodes, SimTKcommon, and Lapack. See the individual projects for descriptions. SimTK brings together in a robust, convenient, open source form the collection of highly-specialized technologies necessary to building successful physics-based simulations of biological structures. These include: strict adherence to an important set of abstractions and guiding principles, robust, high-performance numerical methods, support for developing and sharing physics-based models, and careful software engineering. Accessible High Performance Computing We believe that a primary concern of simulation scientists is performance, that is, speed of computation. We seek to build valid, approximate models using classical physics in order to achieve reasonable run times for our computational studies, so that we can hope to learn something interesting before retirement. In the choice of SimTK technologies, we are focused on achieving the best possible performance on hardware that most researchers actually have. In today''s practice, that means commodity multiprocessors and small clusters. The difference in performance between the best methods and the do-it-yourself techniques most people use can be astoundingeasily an order of magnitude or more. The growing set of SimTK Core libraries seeks to provide the best implementation of the best-known methods for widely used computations such as: Linear algebra, numerical integration and Monte Carlo sampling, multibody (internal coordinate) dynamics, molecular force field evaluation, nonlinear root finding and optimization. All SimTK Core software is in the form of C++ APIs, is thread-safe, and quietly exploits multiple CPUs when they are present. The resulting pre-built binaries are available for download and immediate use. Audience: Biosimulation application programmers interested in including robust, high-performance physics-based simulation in their domain-specific applications.

Proper citation: SimTKCore (RRID:SCR_008268) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mirplant/

A user-friendly plant miRNA prediction tool.

Proper citation: miRPlant (RRID:SCR_012105) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/chibe/

An editing and visualization software tool for pathway models represented by the BioPAX format, using SBGN Process Description Language, based on Chisio.

Proper citation: ChiBE (RRID:SCR_012110) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dical-ibd/

Software tool for detecting identity-by-descent (IBD) tracts between pairs of genomic sequences.

Proper citation: diCal-IBD (RRID:SCR_012111) Copy   

•   Source: SciCrunch Registry

http://sketchel.sourceforge.net/

An interactive chemical molecule sketching tool, and molecular spreadsheet data entry application.

Proper citation: SketchEl (RRID:SCR_012082) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mcdl/

A small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation.

Proper citation: MCDL (RRID:SCR_012084) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/searchgui/

Software providing a user-friendly, lightweight and open-source graphical user interface for configuring and running the freely available OMSSA and X!Tandem search engines simultaneously.

Proper citation: SearchGUI (RRID:SCR_012054) Copy   

•   Source: SciCrunch Registry

http://opencobra.sourceforge.net/openCOBRA/Welcome.html

Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods.

Proper citation: COBRApy (RRID:SCR_012096) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngopt/

Software that produces high quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation, and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation, and includes several improvements to read trimming.

Proper citation: A5-miseq (RRID:SCR_012148) Copy   

•   Source: SciCrunch Registry

http://jchempaint.github.io/

Chemical 2D structure editor and viewer application/applet based on the Chemistry Development Kit (CDK).

Proper citation: JChemPaint (RRID:SCR_000095) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowCL.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for semantic labelling of flow cytometric cell populations.

Proper citation: flowCL (RRID:SCR_000046) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/cbrowse/

Software providing an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs.

Proper citation: Cbrowse (RRID:SCR_000044) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/data/annotation/html/RmiR.Hs.miRNA.html

Software package for various databases of microRNA Targets.

Proper citation: RmiR.Hs.miRNA (RRID:SCR_000101) Copy   

•   Source: SciCrunch Registry

http://nucleobytes.com/index.php/4peaks

Software application for viewing and editing sequence trace files.

Proper citation: 4Peaks (RRID:SCR_000015) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/metaMA/

Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes.

Proper citation: metaMA (RRID:SCR_000408) Copy   

•   Source: SciCrunch Registry

http://www.ks.uiuc.edu/Research/vmd/

A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

Proper citation: Visual Molecular Dynamics (RRID:SCR_001820) Copy   

•   Source: SciCrunch Registry

http://www.liu.se/hu/mdl/main/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An on-line database and publically accessible depository that is dedicated to the omics of small biomolecules.

Proper citation: NMR metabolomics database of Linkoping (RRID:SCR_002758) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/RMassBank.html

Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Proper citation: RMassBank (RRID:SCR_002797) Copy   

•   Source: SciCrunch Registry

http://owlsim.org

Software package that provides the ability to do a number of standard semantic similarity methods and includes novel methods for combining these with dynamic selection of anonymous grouping classes. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: OwlSim (RRID:SCR_006819) Copy   

•   Source: SciCrunch Registry