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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Community building portal that serves over 3,000 members from more than 70 countries by addressing scientific policies, providing access to high quality publications, organizing meetings, and serving as a portal to information about training, education, employment, etc.
Proper citation: International Society for Computational Biology (RRID:SCR_012009) Copy
http://sourceforge.net/projects/exorca/
A Matlab package extending the scope of established COBRA metabolic modelling.
Proper citation: ORCA (RRID:SCR_012097) Copy
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
http://knowtator.sourceforge.net/
A general-purpose text annotation tool that is integrated with the Prot����g���� knowledge representation system.
Proper citation: Knowtator (RRID:SCR_012099) Copy
Online community for industry news and careers for life science professionals.
Proper citation: BioSpace (RRID:SCR_012010) Copy
http://sourceforge.net/projects/pb-jelly/
Software that automates the finishing process using long sequence reads in a reference-guided assembly process.
Proper citation: PBJelly (RRID:SCR_012091) Copy
https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/AHA
Contigs from a draft assembly generated by a different assembler can be joined using PacBio long reads.
Proper citation: AHA (RRID:SCR_012090) Copy
https://code.google.com/p/netcoffee/
A fast and accurate algorithm which allows to find a global alignment of multiple protein-protein interaction networks.
Proper citation: NetCoffee (RRID:SCR_012095) Copy
https://code.google.com/p/qsimscan/
A flexible open source protein similarity search software tool which provides a significant gain in speed compared to BLASTP at the price of controlled sensitivity loss.
Proper citation: PSimScan (RRID:SCR_012094) Copy
http://tfclass.bioinf.med.uni-goettingen.de/tfclass
Database that classifies human transcription factors based on the characteristics of their DNA-binding domains. It comprises six levels (superclasses, classes, families, subfamilies, genera and factor species), two of which are optional (subfamilies and factor species). The full classification can also be obtained as html document and as ontology in obo-format., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: TFClass (RRID:SCR_012018) Copy
http://www.few.vu.nl/~mavdwiel/ShrinkBayes.html
Software for detecting differential features across the entire spectrum, including the lower counts.
Proper citation: ShrinkSeq (RRID:SCR_012022) Copy
A genome browser specialized in next-generation sequencing data.
Proper citation: GenomeJack (RRID:SCR_012026) Copy
Specializes in sequence and array-based SNP and copy number analysis, genetic association software, and analytic services. Their technologies empower scientists to determine the genetic causes of disease, transform drug discovery, develop genetic diagnostics, and advance the quest for personalized medicine.
Proper citation: Golden Helix Incorporated (RRID:SCR_012191) Copy
https://code.google.com/p/glycanbuilder/
An intuitive and flexible software tool for building and displaying glycan structures.
Proper citation: GlycanBuilder (RRID:SCR_012123) Copy
https://code.google.com/p/glycresoft/
A software package for automated recognition of glycans from LC/MS data.
Proper citation: GlycReSoft (RRID:SCR_012122) Copy
Proper citation: Ministry of Health and Family Welfare - Government of India (RRID:SCR_012124) Copy
Public research university in the Australian state of Western Australia. The university's main campus is in Perth, the state capital, with a secondary campus in Albany and various other facilities elsewhere.
Proper citation: University of Western Australia; Perth; Australia (RRID:SCR_012342) Copy
http://www.scienceexchange.com/facilities/bioseek
BioSeek is a drug discovery services company that applies human primary cell assays and predictive disease models to the discovery and development of human therapeutics and safer chemicals. BioSeek improves the success rate of drug discovery and development by integrating human biology from the earliest stages of drug discovery onward through its unique BioMAP??????? platform. Our mission is to accelerate drug compound validation and enable our clients to take safer and more effective products into the market.
Proper citation: BioSeek (RRID:SCR_012224) Copy
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
http://www.iitcinc.com/Plantar.html
The IITC Plantar Analgesia Meter for thermal paw can be used on 12 mice, 6 rats and other animals (cats, rabbits) unrestrained when testing for narcotic drugs. Experiments are easy to perform, simply slide the test head under test subject, align the heat source via our exclusive guide light (idle state) by the attached, adjustable, angled mirror on test head to test subject and perform tests.
Proper citation: IITC Life Sciences: Plantar Test Apparatus (RRID:SCR_012152) Copy
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