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

R package providing functions to assess and to compare the performance of risk prediction (survival) models.

Proper citation: SurvComp (RRID:SCR_003054) Copy   

•   Source: SciCrunch Registry

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

Software that aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation).

Proper citation: Parametric Time Warping (RRID:SCR_003053) Copy   

•   Source: SciCrunch Registry

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

An interactive, user-editable genetic sequence database tool, targeted at molecular biology research groups that can be browsed using tags. The tool is Web 2.0-flavoured, allowing users to do more than just retrieve information. Its focus on user-editability is supported by the use of tags (metadata) associated with genetic sequences. Several methods of retrieving stored data are available including tag-clouds, BLAST and keyword searches. Also, sequence tags related to HGNC gene names, conserved domains (CDD) and GO terms can be automatically generated given sequence data. The tool is constructed using the high-level Python web framework, Django, with a SQLite3 backend.

Proper citation: Gutentag (RRID:SCR_003051) Copy   

•   Source: SciCrunch Registry

http://bodb.usc.edu/bodb/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. BODB offers a way to document computational models of brain function by linking each model to Brain Operating Principles (BOPs), related brain regions, Summaries of Simulation Results (SSRs)and Summaries of Experimental Data (SEDs) used either to design or to test the model. Tools are provided to search for related models and to compare their coverage of SEDs. This allows automatic benchmarking of a model against a cluster of models addressing similar BOPs or SEDs or brain regions. Tools allow display of brain imaging results against a human brain applet; a new tool will link data to a macaque brain applet.

Proper citation: Brain Operation Database (RRID:SCR_003050) Copy   

•   Source: SciCrunch Registry

http://briansimulator.org/

Software Python package for simulating spiking neural networks. Useful for neuroscientific modelling at systems level, and for teaching computational neuroscience. Intuitive and efficient neural simulator.

Proper citation: Brian Simulator (RRID:SCR_002998) Copy   

•   Source: SciCrunch Registry

http://developingmouse.brain-map.org/

Map of gene expression in developing mouse brain revealing gene expression patterns from embryonic through postnatal stages. Provides information about spatial and temporal regulation of gene expression with database. Feature include seven sagittal reference atlases created with a developmental ontology. These anatomic atlases may be viewed alongside in situ hybridization (ISH) data as well as by itself.

Proper citation: Allen Developing Mouse Brain Atlas (RRID:SCR_002990) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/pacBioToCA

A module in the Celera Assembler software package that performs error correction on PacBio long reads by mapping shorter, high accuracy reads onto the long reads.

Proper citation: PacBioToCA (RRID:SCR_003044) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/R-pbutils

An R software package providing plotting and convenience functions.

Proper citation: R-pbutils (RRID:SCR_002995) Copy   

•   Source: SciCrunch Registry

http://bibiserv.techfak.uni-bielefeld.de/dialign/

Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/

Proper citation: DIALIGN (RRID:SCR_003041) Copy   

•   Source: SciCrunch Registry

http://www.dana-farber.org/

Cancer institute that provides expert, compassionate care to children and adults with cancer while advancing the understanding, diagnosis, treatment, cure, and prevention of cancer and related diseases. As an affiliate of Harvard Medical School and a Comprehensive Cancer Center designated by the National Cancer Institute, the Institute also provides training for new generations of physicians and scientists, designs programs that promote public health particularly among high-risk and underserved populations, and disseminates innovative patient therapies and scientific discoveries to their target community across the United States and throughout the world.

Proper citation: Dana-Farber Cancer Institute (RRID:SCR_003040) Copy   

•   Source: SciCrunch Registry

http://deweylab.biostat.wisc.edu/psginfer/

Software for inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.

Proper citation: PSGInfer (RRID:SCR_000243) Copy   

•   Source: SciCrunch Registry

http://www.structbioinfor.org/cascleave2/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A novel tool developed using Java program for the high-throughput in silico identification of substrate cleavage sites for various caspases from the amino acid sequences of the substrates.

Proper citation: Cascleave (RRID:SCR_000197) Copy   

•   Source: SciCrunch Registry

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

Software package that fits heterogeneous error models for analysis of microarray data

Proper citation: HEM (RRID:SCR_000194) Copy   

•   Source: SciCrunch Registry

http://www.aetionomy.eu/

Consortium founded to establish mechanism-based taxonomies for Alzheimer's and Parkinson's disease and other neurodegenerative disorders (NDD), with the goal of facilitating development of more effective and targeted treatments. To do this, the consortium collects and analyzes data to: * Create new ways to combine underutilized data currently available in the literature, public databases, and from private companies * Determine how to dynamically organize and structure different types of knowledge about NDD * Determine how to apply this knowledge to construct new patient group classification * Identify correlations between disease features at molecular, tissue or organ-specific, and clinical levels * Identify sub-groups of patients based on the molecular cause of their disease, as opposed to the nature and location of their symptoms * Deliver data, tools, and recommendations for the biomedical community in the treatment of NDD A mechanism-based taxonomy is hoped to advance the: # Description and organization of the indication-specific data # Linking of data to disease models, based on causal and correlative relationships The expected outcome of AETIONOMY is a new NDD taxonomy system that distinguishes mixed pathologies, allowing for new features or classes to be added into the taxonomy, all with the goal of aiding drug and biomarker discovery.

Proper citation: AETIONOMY (RRID:SCR_000232) Copy   

•   Source: SciCrunch Registry

http://molegro-virtual-docker.software.informer.com/

An integrated platform for predicting protein-ligand interactions, the visualization of new ideas and analyzing protein targets.

Proper citation: Molegro Virtual Docker (RRID:SCR_000190) Copy   

•   Source: SciCrunch Registry

http://www.zju.edu.cn/english/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A public research university with twelve main academic disciplines that include science, engineering, agriculture and medicine. The university has campuses across China in locations such as Yuquan, Zhijiang and Zhoushan. It has studies available in undergraduate, graduate and post-doctorate degrees.

Proper citation: Zhejiang University; Zhejiang; China (RRID:SCR_000224) Copy   

•   Source: SciCrunch Registry

http://www.paradyn.org/mrnet/

A software-based network that provides efficient multicast and reduction communications for parallel and distributed tools and systems. Some key features of this resource include scalable data aggregation, multiple concurrent data channels and high-bandwidth communication.

Proper citation: MRNet (RRID:SCR_000225) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/

Software that allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

Proper citation: FastQ Screen (RRID:SCR_000141) Copy   

•   Source: SciCrunch Registry

http://deweylab.biostat.wisc.edu/rsem/

Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data.

Proper citation: RSEM (RRID:SCR_000262) Copy   

•   Source: SciCrunch Registry

http://www.tcd.ie/

A public university, which is a part of the University of Dublin, and contains three main academic disciplines: Arts, Humanities and Social Sciences; Engineering, Mathematics and Sciences; and Health Sciences. The institution offers degrees at the undergraduate and graduate level.

Proper citation: Trinity College Dublin; Dublin; Ireland (RRID:SCR_000261) Copy   

•   Source: SciCrunch Registry