| CLC Protein Workbench
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Linux Mac Windows |
| CLC Protein Workbench 1.5 provides a wide range of advanced protein sequence analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench. Some analyses are - Advanced and integrated 3D molecular viewer - 2 types of alignments - Phylogenetics - Secondary protein structure prediction - Signal Peptide Prediction (SignalP) - Transmembrane helix prediction (TMHMM) - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Protein family analysis (PFAM) - Dot plots - Hydrophobicity analyses - Antigenicity analyses - Searches on GenBank, Swiss-Prot, TrEMBL, and PubMed - Detailed log of actions/analyses performed |
 Web Site: CLC bio
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| CLC RNA Workbench
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Linux Mac Windows |
| CLC RNA Workbench aggregates a large number of advanced RNA sequence analyses and other bioinformatics analyses in one single, integrated, user-friendly, and intuitive software application. Some features are Secondary RNA structure prediction, Graphical view and editing of secondary RNA structures, Tabular view of RNA structures and RNA energy contributions, Symbolic representation of RNAs in sequence view, Pattern search, Search for sequence matches, Motif search for basic patterns, Motif search using regular expressions, Motif search with ProSite patterns, Pattern discovery (unknown patterns), Project and data management, Detailed history log, All types of files can be saved in local projects, and launched from the program, DNA, RNA and protein sequence editor displaying both linear and circular molecules, Multiple alignment of DNA, RNA, and proteins: ClustalW, Muscle, T-Coffee, MAFFT, Kalign. Interactive logo graphs along both DNA, RNA and Protein alignments, BLAST, and much more. |
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Web Site: www.clcbio.com
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| COSY, SYNDAT, MODFUN and SIMKIN 4.0
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MS-DOS |
| Enzyme kinetics package. SYNDAT is used to generate data according to a model function with fixed parameters. COSY is a program for analysis of kinetic and equilibrium data. MODFUN evaluates the result and the derivatives with respect to fit parameters of each of the defined model functions. SIMKIN offers the possibility to simulate kinetic mechanisms. |
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Download (1538 kb, 06-Feb-1991) |
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| Cell Composition Toolbook
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Windows |
| This set of programs, authored with Asymetrix Toolbook, provides a basic tutorial covering the chemical composition of the cell. It is designed for use at first year level as a revision aid to complement the introduction of basic chemistry in the context of simple biological systems. |
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Web Site: BioNet
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| Cell Illustrator
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Linux Mac Unix Windows |
| Cell Illustrator is a tool for constructing pathway models and simulating pathway mechanisms of action of both baseline and abnormal conditions. The Software provides biochemists with comprehensive visual representations of biochemical processes which form large and complex networks. It gives new insight to understanding these networks and relationships between chemical components in structurally complex dynamic interactions and processes. |
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Web Site: More Information about Cell Illustrator
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| ChemTree HTS Analysis Software
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Linux Mac Unix Windows |
| Offering univariate and multivariate recursive partitioning data mining software customized to the field of HTS and QSAR. Builds structure activity models on screening data to understand 'mechanisms of action', and drive the sequential screening compound optimization process. Nodel tree generation facilitates |
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Web Site: Golden Helix, Inc.
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| Chemfont
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Windows |
| A Windows font package that simplifies the entry of chemical equations. |
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Web Site: Bio-Rad Laboratories
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| CryoTrack IMS
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Windows |
| CryoTrackIMS is a complete software package - ideal for molecular biology, cell banks, cellular biology, clinical samples, chemical labs, biochemistry, immunology and protein labs, high-throughput screening, QA, IVF labs and core facilities. Suitable for all storage formats and locations such as liquid nitrogen, freezers, refrigerators and room temperature storage. |
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Web Site: CryoTrack Sample Tracking Software
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| CrystalMaker
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Mac Windows |
| CrystalMaker is an award-winning program for building, displaying and manipulating all kinds of crystal and molecular structures - with real-time photo-realistic graphics and |
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Web Site: CrystalMaker Software Ltd
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| DIG - Analysis, Reporting, Intelligence
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Linux Unix Windows |
| DIG is a Data Analysis, Reporting, Intelligence tool for data workers, labs, and webmasters. Use DIG to clean up duplicates, consolidate, trim, query, summarize large data set in Excel/Access, log files, Oracle, MySQL, lab or POS systems, or any databases. Comes with powerful Excel/Access add-ons, ad-hoc query & multi-dimensional analysis. Watch on-line demo, get a free 30-day trial, then pay $96/yr or $8/month. |
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Web Site: DigDB
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| Database of Macromolecular Movements
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Internet Browser |
| Searchable database of the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis. |
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Web Site: Yale University
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| EZ-FIT 1.1
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MS-DOS |
| EZ-FIT is an interactive computer software package that fits experimental data to a variety of model equations. Useful for calculation of enzyme and receptor kinetics. |
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Download (125 kb, 18-Oct-1989) |
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| Enzyme: Enzyme Nomenclature Database
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Internet Browser |
| ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided. |
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Web Site: Expasy
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| EnzymeKin 1.0
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Mac |
| Calculation of enzyme kinetics. |
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Download (105 kb, 22-Sep-1989) |
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| Equilibrate
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Windows |
| This software can be used as a scientific or educational tool in biochemistry and molecular biology for quantitative analysis of molecular interactions. The program calculates equilibria and dissociation constants for interacting molecules. |
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Web Site: Veenstra
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| Expression
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Windows |
| Expression is a revolutionary new application for DNA and protein sequence analysis. Utilising a novel interface, Expression makes complex computational analyses of sequence information incredibly simple. Expression uses the very latest computing technology to set new standards in the way sequences are analysed. Features include: Sequence Annotation,Graphical Sequence Map, Degenerate DNA and Amino Acid Sequence Support, Restriction Analysis, Primer Design and Analysis, ORF Prediction, Pattern Finding, Reverse Translation, GenBank Searching, Pattern and Motif Identification, Multiple Sequence Alignment, and Protein Structure Prediction. |
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Web Site: Genamics
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| FLUENT
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Windows |
| Fluent is the world's largest provider of computational fluid dynamics (CFD) software and consulting services. Fluent's software is used for simulation, visualization, and prediction of fluid flow, heat and mass transfer, and chemical reactions. Using Fluent's software, product development and research engineers build virtual prototypes and simulate the performance of proposed and existing designs, which helps them to optimize, troubleshoot, scale-up, and retrofit. Use of CFD software reduces time-to-market by reducing the need for costly physical testing and prototyping. |
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Web Site: Fluent Incorporated
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| Fast chromatogram viewer
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Windows |
| This freeware tool will list all chromatogram files (SCF, ABI, AB1, AB) in the current folder. You can view the chromatogram by simply clicking a file. Install process: You do not need to install it. Just download the program and double click to run it. It does not need additional software, updates, DLLs or Java to run it. To uninstall it just delete the program. |
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Web Site: Fast chromatogram viewer
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| FermWorks
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Internet Browser Linux Mac Unix Windows |
| Fermentation process control software that integrates cell culture and fermentation research for comprehensive process management. FermWorks bioreactor and fermentor software exposes data for control and analysis of processes. Provides real-time control and monitoring. Integrates all sources of data associated with an experiment. Controls a wide variety of instruments and hardware. Adapts to diverse laboratory and pilot plant environments. Researchers may customize trending tools, recipes, protocols, and control algorithms. Allows for the easy introduction of custom features and calculations. Allows existing subroutines to run as plug-in code for customized control. Distributes data across secure networks. Provides web access for monitoring processes, generating reports, analyzing data, and configuring experiments. Links workstations, archives, and enterprise systems. Data from workstations are available as process values for any experiment on the network. Plug-ins are made available to all bioreactors on a network. |
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Web Site: Jova Solutions
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| GENtle
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Windows |
| GENtle is a program for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, specialized calculators, PCR, gel image display, virtual gel simulation, and more. |
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| GEPASI 2.08a
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MS-DOS |
| GEPASI 2.0, a general purpose simulator of metabolic pathways. It is a directed towards research and education; it is meant to be a very useful tool for modelling biochemical pathways, system kinetics chemical reactions,etc. |
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Web Site: Gepasi
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Download (595 kb, 06-Sep-1993) |
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| GelQuest
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Windows |
| Software for the analysis of DNA fingerprint data: AFLP, RFLP, tRFLP, RAPD. GelQuest imports trace data (FSA files) from automtic sequencers as well as images from slab gels. It performs peak detection, fragment sizing using size standard matching and binning (bins, superbins, hyperbins). Exports data as trace files, tab-delimited spread sheaths, 01 matrix, Nexus, Newick and other formats. |
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Web Site: GelQuest DNA Fingerprint Software
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| GenScript siRNA Target Finder
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Internet Browser |
| To facilitate the designing process for vector-based siRNA and siRNA cassette, a tool set has been developed: siRNA target finder, siRNA construct builder, and siRNA sequence scrambler. The siRNA target finder is used to identify candidate siRNA target sites. The program automates homology filtering, minimizes non-specific cross-reaction, filters target sites based on RNA duplex internal stability and siRNA sense/anti-sense strand secondary structure. The siRNA construct builder is used to create siRNA hairpin construct as vector insert or cassette insert. The siRNA sequence scrambler is used to generate negative control sequence for siRNA experiment. Together, these programs provide a comprehensive utility set to address the specific bioinformatics need of DNA-based siRNA design. |
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Web Site: GenScript siRNA Target Finder
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| Gene and Protein Synonym DataBase (GPSDB)
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Internet Browser |
| GPSDB (Gene and Protein Synonym DataBase) is the most comprehensive collection of gene and protein name synonyms, organized by species. Freely accessible on the web. Published by PharmaDM. |
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Web Site: BioMinT
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| GenomatixSuitePE
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Internet Browser Linux Mac Unix Windows |
| GenomatixSuitePE enables biologists to discover, explore and understand biologically relevant pathways down to the molecular level. Applying the GenomatixSuitePE pipeline to a researcher's set of genes e. g. from a microarray analysis, generates the full biological network, allowing for functional analysis of the most relevant sub-network and enables understanding of gene regulatory mechanisms on DNA sequence level. |
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Web Site: Genomatix
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