Curator Dashboard

Mass spectral peak labeling software developed for proteomics research., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 12 years ago - by Anonymous

A DNA reads trimming software, written in Java, with which researchers are able to analyse the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way.

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• SciCrunch
• 12 years ago - by Anonymous

A single source for sequences, assemblies, annotations and analyses of the genomes of members of the fruitfly genus Drosophlia. It is meant as resource for Drosophilists and other researchers interested in comparative analysis of these species and their genomes. There are pages for each species, as well as pages for different types of multi-species resources (e.g. alignments). If you have a public resource that will help this project, please consider making it available through this page by emailing multiple_at_fruitfly.org.

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• SciCrunch
• 17 years ago - by Anonymous

Database built upon genomic annotation of splicing patterns of known genes derived from spliced alignment of complementary DNAs (cDNAs) and expressed sequence tags for human and mouse. It links features such as splice site sequence and strength, exonic splicing enhancers and silencers, conserved and non-conserved patterns of splicing, and cDNA library information for inferred alternative exons. A query tool allows searches for sets of exons with specific splicing characteristics or splicing regulatory element composition, or gives a graphical or sequence-level summary of splicing patterns for a specific gene. A graphical representation of gene splicing patterns is provided, and these patterns can alternatively be layered onto existing information in the UCSC Genome Browser.

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• SciCrunch
• 13 years ago - by Anonymous

The Lafora database is a repository of information related to progressive myoclonus epilepsy mutation and polymorphism data. Users may view all mutations in the database(Mutations of EPM2A and NHLRC1(EPM2B)), click on individual exons for mutations, or search the database by keyword. Nucleotide and amino acids positions were assigned based on the GenBank reference sequence NM_005670 for EPM2A and NM_198586 for EPM2B. The data can be viewed using the XRT Table Browser, and where possible, links to external sources such as NCBI, PubMed are provided. At this time, the database is under development. The BioXRT (Cross-Referenced Tables) Table Browser is a highly configurable tool for viewing complex, table based information. The tables can be displayed using pre-set options, or customized to view arbitrary subsets of rows, columns or other features.

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• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Software package for convex optimization based on the Python programming language. It can be used with the interactive Python interpreter, on the command line by executing Python scripts, or integrated in other software via Python extension modules. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Pythons extensive standard library and on the strengths of Python as a high-level programming language. Current version includes the following features: * efficient Python classes for dense and sparse matrices (real and complex), with Python indexing and slicing and overloaded operations for matrix arithmetic * an interface to most of the double-precision real and complex BLAS * an interface to LAPACK routines for solving linear equations and least-squares problems, matrix factorizations (LU, Cholesky, LDLT and QR), symmetric eigenvalue and singular value decomposition, and Schur factorization * an interface to the fast Fourier transform routines from FFTW * interfaces to the sparse LU and Cholesky solvers from UMFPACK and CHOLMOD * routines for linear, second-order cone, and semidefinite programming problems * routines for nonlinear convex optimization * interfaces to the linear programming solver in GLPK, the semidefinite programming solver in DSDP5, and the linear, quadratic and second-order cone programming solvers in MOSEK * a modeling tool for specifying convex piecewise-linear optimization problems. A platform-independent source package and a binary Windows installer are available from the Download section. CVXOPT is also available precompiled for the major platforms: * Debian Linux * Ubuntu Linux * Fedora Linux * Python(x,y) for Microsoft Windows CVXOPT is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.

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• SciCrunch
• 15 years ago - by Anonymous

A bioinformatics platform that is a joint project of several South of France laboratories with available services based on their expertise, issued from their research activities which involve phylogenetics, population genetics, molecular evolution, genome dynamics, comparative and functional genomics, and transcriptome analysis. Most of the software and databases on ATGC are (co)authored by researchers from South of France teams. Some are widely used and highly cited. South of France laboratories: * CRBM (transcriptomes and stem cells). * IBC (computational biology). * MiVEGEC (evolution and phylogeny). * LGDP (plant genomics). * LIRMM (computer science). * South Green (plant genomics).

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• SciCrunch
• 17 years ago - by Anonymous

Simulation software that includes a parallel discrete event simulation kernel for running models of spiking neurons on a cluster of workstations. Models are specified using NeuroML, and visualized using Java2D. Simulation components are distributed across a parallel machine or network and communicate using timestamped events. The successor NEOSIM2 project under the NeuroGems umbrella at Edinburgh University (http://www.neurogems.org) continues to distribute the software, http://www.neurogems.org/neosim2/ The NEOSIM project includes: * a parallel discrete event simulation kernel for running models of spiking neural networks on clusters of machines. * a modules kit for extending the behavior of neurons and connectivity patterns. * a user interface for building and running simulations. OS: Linux, MS-Windows

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• SciCrunch
• 17 years ago - by Anonymous

MATLAB toolbox for deep-brain-stimulation (DBS) electrode reconstructions and visualizations based on postoperative MRI and computed tomography (CT) imaging. The toolbox also facilitates visualization of localization results in 2D/3D, analysis of DBS-electrode placement's effects on clinical results, simulation of DBS stimulations, diffusion tensor imaging (DTI) based connectivity estimates, and fiber-tracking from the VAT to other brain regions (connectomic surgery).

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• SciCrunch
• 12 years ago - by Anonymous

Contract Research Org. specializing in custom protein analysis. Services Provided include SDS PAGE analysis, Western Blotting, Mass Spectrometry, protein staining ( silver,coomassie) for academia, federal institutions and industry.

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• SciCrunch
• 17 years ago - by Anonymous

Database of mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. The mitochondrion plays a central role in cellular metabolism, and evidence of mitochondrial involvement in a number of different human diseases is increasing. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases. Mitochondrial DNA Sequence: A graphical tool was developed to visualize the human mitochondrial DNA sequences that highlight coding regions for RNAs and proteins. Disease susceptible mutations are also noted in the sequence. Mitochondrial DNA Polymorphism: Human mitochondrial sequences of different ethnic groups were obtained from the Human Mitochondrial Genome Database. A DNA sequence analysis tool was developed to compare polymorphisms of different human mitochondrial DNA sequences. This tool allows the user to select mitochondrial sequences from any two human populations and compare them for sequences variations. Mitochondrial proteins related diseases: Malfunction of mitochondrial proteins affect many cells from brain, heart, liver, skeletal muscles, kidney, and the endocrine and the respiratory systems which lead to many diseases. Relevant information for mitochondrial related diseases from OMIM, the Neuromuscular Disease Center and MITOMAP are gathered, and mitochondrion-associated diseases are grouped, categorized, and linked to OMIM. 3-D Structures of Mitochondrial proteins: The available 3D structures for mitochondrial proteins are presented through a custom-made interface. A concise HTML page is generated for reporting the structural details and the associated information obtained from relevant web sites (PDBREPORT, Interatomic Contacts of Structural Units (CSU), PROCHECK, Ligand Protein Contacts (LPC), PROMOTIF and CastP). References are linked to the PubMed site. The 3-D structures are presented through the use of a Kinemage.

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• SciCrunch
• 15 years ago - by Anonymous

Portal that lists and provides information on core facilities located at the University of Florida.

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2025. eGOn is a web-based tool for interpreting and statistical analysis of genomic data or other interesting gene sets using Gene Ontology. eGOn is a graphical, interactive data mining tool. It associates user input reporter lists with GO terms and visualizes such GO terms as a hierarchical tree. Users can manipulate the tree output by various means. Significantly important GO terms resulted from a statistical test can be reported. All related information is exportable. Key features: - User friendly web-based interface and free of charge for academic users - Database storage of reporter lists - Manage submitted reporter lists in folders and sharing opportunities of reporter lists. - Enable filtering on GO evidence codes - Regularly updates of GO and gene annotation data - Fully expandable trees for browsing the GO hierarchy - Direct link to the NTNU Annotation Database for gene annotation information - Possible to add user defined GO annotations - Several statistic testes for analyses within and between reporter lists, indicating GO terms with relatively enriched gene numbers and suggesting biological areas that warrant further study. Result report views with statistical significant GO terms. - Results can be exported in txt, xls or XML format Sponsors: eGOn is developed by the Norwegian Microarray Consortium (NMC) and Department of Cancer Research and Molecular Medicine at Norwegian University of Science and Technology (NTNU).

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• SciCrunch
• 17 years ago - by Anonymous

University of Colorado is a four-campus system that includes the University of Colorado Boulder, the University of Colorado Colorado Springs, the University of Colorado Denver and the University of Colorado Anschutz Medical Campus.

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• SciCrunch
• 17 years ago - submitted by Timothy Tsui

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Command line version of multiple sequence alignment program Clustal for DNA or proteins. Alignment is progressive and considers sequence redundancy. No longer being maintained. Please consider using Clustal Omega instead which accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/ClustalW, GCG/MSF, RSF.

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• SciCrunch
• 17 years ago - by Anonymous

ISCoS promotes the highest standard of care in the practice of spinal cord injury for men, women and children throughout the world. Through its medical and multi disciplinary team of Professionals ISCoS endeavours to foster education, research and clinical excellence. ISCoS has a membership of over 1,000 Clinicians and Scientists from 87 countries. They regularly update their knowledge at the Annual Scientific Meeting held in a different country each year. Goals of ISCoS: :- Serve as an international impartial, non-political and non-profit making association whose purpose is to study all problems relating to traumatic and non-traumatic lesions of the spinal cord. This includes causes, prevention, basic and clinical research, medical and surgical management, clinical practice, education, rehabilitation and social reintegration. This society will function in close collaboration with other national and international bodies, thereby encouraging the most efficient use of available resources. :- Provide a scientific exchange among its members and others by collecting and disseminating information through publications, correspondence, exhibits, regional and international seminars, symposia, conferences and otherwise. :- Advise, encourage, promote and when requested, assist in efforts to co-ordinate or guide research, development and evaluation activities related to spinal cord lesions throughout the world. :- Advise, encourage, guide and support the efforts of those responsible for the care of patients involved and when requested, correlate these activities throughout the world. :- Advise, encourage, guide and support the efforts of those responsible for the education and training of medical professionals and professionals allied to medicine and when requested, correlate these activities throughout the world.

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• SciCrunch
• 17 years ago - by Anonymous

The Lowe Syndrome Mutation Database is now being maintained by the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. A database of mutations causing Lowe syndrome. Information on new mutations may be submitted online. Lowe oculocerebrorenal syndrome is an X-linked disorder caused by mutations in the OCRL1 gene, which encodes a 105-kDa Golgi protein with phosphatidylinositol (4,5) bisphosphate 5-phosphatase activity. genetics

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. HIV Sequence Database is a database of annotated HIV sequences, plus a variety of tools and information for researchers studying HIV and SIV. The main aim of this website is to provide easy access to our sequence database, alignments, and the tools and interfaces we have produced. The HIV Sequence Database focuses on five primary goals: * Collecting HIV and SIV sequence data (all sequences since 1987) * Curating and annotating this data, and making it available to the scientific community * Computer analysis of HIV and related sequences * Production of software for the analysis of (sequence) data * The data and analyses on this site and published in a yearly printed publication, the HIV sequence Compendium, which is available free of charge.

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• SciCrunch
• 17 years ago - by Anonymous

British charity and fundraiser for cardiovascular research.

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• SciCrunch
• 17 years ago - submitted by Timothy Tsui

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.The HIV Resistance Mutation Database is a resource that allows users to download HIV sequences and information on HIV drug resistance and mutations. Users must download the data from either of two files available on the site, as the online portion of the database is no longer available. The system requires Mac OS9 to work. The DATABASES folder contains the current versions of 2 databases copied from resdb: BestDefined, and resistrelated. The BestDefined database is a list of the Brander epitopes. The resistrelated database is a compilation of HIV drug resistance mutations. The Bib and biblio files are the associated references for these databases. The RESIST_HTML folder contains the html files used by the resistance database web site.

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• SciCrunch
• 17 years ago - by Anonymous