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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://www.onu.edu/

A public university in Ohio with land, sea and space grants that offers degree programs and research at the undergraduate and graduate level.

Proper citation: Ohio Northern University; Ohio; USA (RRID:SCR_000362) Copy   

•   Source: SciCrunch Registry
  

http://ribopicker.sourceforge.net/

Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.

Proper citation: riboPicker (RRID:SCR_000360) Copy   

•   Source: SciCrunch Registry
  

http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development

A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads.

Proper citation: ARACHNE (RRID:SCR_000351) Copy   

•   Source: SciCrunch Registry
  

http://parsecnv.sourceforge.net/

Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance.

Proper citation: ParseCNV (RRID:SCR_000355) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/kinannote/

Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com.

Proper citation: Kinannote (RRID:SCR_000352) Copy   

•   Source: SciCrunch Registry
  

http://www.scienceexchange.com/facilities/genomics-services-lab

A lab that offers genetic research tools such as RNA sequencing and a variety of arrays.

Proper citation: HudsonAlpha Genomics Services Lab (RRID:SCR_000353) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/jnomics/

A collection of cloud-scale DNA sequence analysis tools.

Proper citation: Jnomics (RRID:SCR_000348) Copy   

•   Source: SciCrunch Registry
  

http://www.abrowse.org/

A genome browser framework which gives an open browsing experience, open data access, collaborative work support, and a framework to import annotations. Multiple data access approaches are supported for external platforms to retrieve data from ABrowse. This resource also contains an online user-space in which users can create, store and share comments, annotations and landmarks.

Proper citation: ABrowse (RRID:SCR_000345) Copy   

•   Source: SciCrunch Registry
  

http://icbi.at/software/gpviz/gpviz.shtml

A versatile Java-based software used for dynamic gene-centered visualization of genomic regions and/or variants.

Proper citation: GPViz (RRID:SCR_000346) Copy   

•   Source: SciCrunch Registry
  

http://teddy.epi.usf.edu/

International consortium of six centers assembled to participate in the development and implementation of studies to identify infectious agents, dietary factors, or other environmental agents, including psychosocial factors, that trigger type 1 diabetes in genetically susceptible people. The coordinating centers recruit and enroll subjects, obtaining informed consent from parents prior to or shortly after birth, genetic and other types of samples from neonates and parents, and prospectively following selected neonates throughout childhood or until development of islet autoimmunity or T1DM. The study tracks child diet, illnesses, allergies and other life experiences. A blood sample is taken from children every 3 months for 4 years. After 4 years, children will be seen every 6 months until the age of 15 years. Children are tested for 3 different autoantibodies. The study will compare the life experiences and blood and stool tests of the children who get autoantibodies and diabetes with some of those children who do not get autoantibodies or diabetes. In this way the study hopes to find the triggers of T1DM in children with higher risk genes.

Proper citation: TEDDY (RRID:SCR_000383) Copy   

•   Source: SciCrunch Registry
  

http://www.tarp.nih.gov/

Trans-NIH program encouraging and facilitating the study of the underlying mechanisms controlling blood vessel growth and development. Other aims include: to identify specific targets and to develop therapeutics against pathologic angiogenesis in order to reduce the morbidity due to abnormal blood vessel proliferation in a variety of disease states; to better understand the process of angiogenesis and vascularization to improve states of decreased vascularization; to encourage and facilitate the study of the processes of lymphangiogenesis; and to achieve these goals through a multidisciplinary approach, bringing together investigators with varied backgrounds and varied interests.

Proper citation: Trans-Institute Angiogenesis Research Program (RRID:SCR_000384) Copy   

•   Source: SciCrunch Registry