Tools   Select Another Resource Report Type

https://github.com/yhwu/matchclips/

Software program that detects the precise break points of Copy number variations (CNVs) through a fuzzy string matching algorithm using both CIGAR and POS information. In case the two break points of a CNV are in repeated regions and the break points are not unique, it reports the range where the break points can slide.

Proper citation: MATCHCLIP (RRID:SCR_000541) Copy   

•   Source: SciCrunch Registry

http://www.exonhit.com/

A drug and diagnostic discovery company.

Proper citation: Exonhit Therapeutics (RRID:SCR_000493) Copy   

•   Source: SciCrunch Registry

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

Software package to infer gene regulatory networks from time-series measurements. The algorithm is expected to be useful in reconstruction of small biological directed networks from time course data.

Proper citation: TDARACNE (RRID:SCR_000498) Copy   

•   Source: SciCrunch Registry

http://scicrunch.org/Aging

Portal devoted to aging relevant scientific data and resources.

Proper citation: Aging Portal (RRID:SCR_000496) Copy   

•   Source: SciCrunch Registry

http://gtr.rcuk.ac.uk/project/239F234A-6BF7-4E28-8964-E882BAA8EB77

Project aiming to establish a range of new technologies to enable the synthesis of a range of chemicals from sugar beet pulp (SBP) in a cost-effective and sustainable manner. The chemical and pharmaceutical industries are currently reliant on petrochemical derived intermediates for the synthesis of a wide range of valuable products. Decreasing petrochemical reserves and concerns over costs and greenhouse gas emissions are driving the search for renewable sources of organic synthons. The UK is self-sufficient in the production of SBP which is a by-product of sugar beet production (8 million tonnes grown per year) and processing. The ability to convert SBP into chemicals and pharmaceutical intermediates will therefore have significant economic and environmental benefits. SBP is rich in carbohydrate (nearly 80% by weight) which is made up of roughly equal proportions of 2 biological polymers; cellulose and pectin. To be cost-effective it will be necessary to find uses for each of these substances. The consortium will develop a biorefinery approach for the selective breakdown of both polymers, purification of the breakdown compounds and their use to synthesize a range of added value products such as speciality chemicals, pharmaceuticals and biodegradable polymers. It is already known that cellulose can be broken down into hexose sugars and fermented to ethanol for use in biofuels. The focus is on the release of galacturonic acid and arabinose (from pectin) and their conversion, by chemical or enzymatic means, into added value products. Synthetic Biology methods will also be explored to test the feasibility of metabolically engineering microbial cells to simultaneously breakdown the polymeric feed material and synthesize a desired product, such as aromatic compounds, in a single integrated process. In conducting this research the consortium will adopt a holistic, systems-led, approach to biorefinery design and operation. Computer-based modelling tools will be used to assess the efficiency of raw material, water and energy utilization. Economic and Life Cycle Analysis (LCA) approaches will then be employed to identify the most cost-effective and environmentally benign product and process combinations. The project is supported by a range of industrial partners from raw material producer to intermediate technology providers and end-user chemical and pharmaceutical companies. This is crucial in providing business and socio-economic insights regarding the adoption of renewable resources into their current product portfolios. The company partners will also provide the material and equipment resources for the large-scale verification of project outcomes and their ultimate transition into commercial manufacture. The Intellectual Property (IP) expected to be generated by the consortium will most likely be related to new biocatalysts, synthetic routes, USD devices and modelling software. The data is accessible programmatically using one of three application programming interfaces GtR, GtR-2 and CERIF.

Proper citation: Bio-derived Feedstocks for Sustainable UK-Based Manufacture of Chemicals and Pharmaceutical Intermediates (RRID:SCR_000490) Copy   

•   Source: SciCrunch Registry

http://mfuzz.sysbiolab.eu/

Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Mfuzz (RRID:SCR_000523) Copy   

•   Source: SciCrunch Registry

http://gmt.genome.wustl.edu/pindel/0.2.4/

Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Pindel (RRID:SCR_000560) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/ontomorphtab/

OntoMorph is a tab plugin for Protege-OWL 3 that allows a user to mark-up portions of a Neurolucida neuron morphology with OWL instances. A user loads a Neurolucida morphology file, either from their hard drive or from an arbitrary URL, into an interface that allows them to zoom, rotate, and translate the morphology. The interface allows them to select points on the morphology to indicate points, segments, or subtrees of the morphology they wish to assign to an OWL instance. After this selection has been made, OntoMorph saves the selection to the currently active OWL instance in the ontology that is currently loaded into Protege. No modifications are made to the Neurolucida file itself. As a result, an association is created between that portion of the morphology and the OWL instance, such that selecting the OWL instance allows retrieval of the portion. Upon retrieval, the morphology portion can be highlighted, so the user can keep track of what pieces each instance refer to.

Proper citation: OntoMorph Tab (RRID:SCR_000443) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/genome_bio/siphy/

Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions.

Proper citation: SiPhy (RRID:SCR_000564) Copy   

•   Source: SciCrunch Registry

http://edwards.sdsu.edu/scaffold_builder/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool designed to generate scaffolds (super contigs of sequences joined by N-bases) using the homology provided by a closely related reference sequence. Scaffold_builder is an advanced wrapper for Nucmer, written in Python that resolves several situations that may arise when mapping contigs to the reference genome.

Proper citation: Scaffold builder (RRID:SCR_000556) Copy   

•   Source: SciCrunch Registry

http://lilab.stanford.edu/SNPiR/

Software for reliable Identification of Genomic Variants Using RNA-seq Data.

Proper citation: SNPiR (RRID:SCR_000557) Copy   

•   Source: SciCrunch Registry

http://paleogenomics.irmacs.sfu.ca/FPSAC/

Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs.

Proper citation: FPSAC (RRID:SCR_000555) Copy   

•   Source: SciCrunch Registry

http://bbc.mdc-berlin.de/software

Multi-purpose SNV calling software enhanced by probabilistic integration of quality scores.

Proper citation: ACCUSA2 (RRID:SCR_000558) Copy   

•   Source: SciCrunch Registry

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

Software for Greedy Clustering of 16S rRNA Reads which uses a dynamic seeding strategy.

Proper citation: DySC (RRID:SCR_000553) Copy   

•   Source: SciCrunch Registry

https://nei.nih.gov/health/clinicalstudies/

An archived portal of clinical studies, both ongoing and completed, that have been conducted and supported by the National Eye Institute (NEI) since 1970. The portal covers corneal diseases, glaucoma, epidemiology, lens and cataract, retinal diseases, strabismus, amblyopia and visual processing.

Proper citation: NEI Clinical Studies (RRID:SCR_000546) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/popbam/

A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome.

Proper citation: POPBAM (RRID:SCR_000464) Copy   

•   Source: SciCrunch Registry

http://drfast.sourceforge.net/

A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner.

Proper citation: drFAST (RRID:SCR_000586) Copy   

•   Source: SciCrunch Registry

http://genome.crg.es/software/gfftools/GFF2PS.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format.

Proper citation: Genome BioInformatics Research Lab - gff2ps (RRID:SCR_000462) Copy   

•   Source: SciCrunch Registry

http://bioinfo2.ugr.es/NGSmethPipe/

A software tool which generates high-quality methylation maps.

Proper citation: NGSmethPipe (RRID:SCR_000583) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/src/contrib/Archive/sybil/

A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). This is an implementation of COBRA toolbox in R language.

Proper citation: sybil - Efficient Constrained Based Modelling in R (RRID:SCR_000457) Copy   

•   Source: SciCrunch Registry