MARTINDALE'S CALCULATORS ON-LINE CENTER SCIENCE A-Z BIOSCIENCE

US/Pacific: Sunday, October 24, 2004 Sydney, Australia: Monday, October 25, 2004 File Download Time Calculator Author, E-Mail, Privacy Policy & Disclaimer Currently the Calculators On-Line Center contains over "18,795" Calculators

Axon Potential AXON POTENTIAL SIMULATOR AXON POTENTIAL SIMULATOR (JAVA APPLET) - J.L. Ram, Department of Physiology, School of Medicine, Wayne State University, Detroit, Michigan VERY VERY EXTENSIVE. "...a Hodgkin-Huxley membrane potential simulation." "...can be used for simulating action potentials, synaptic potentials and their interactions, current injection, voltage clamping, effects of changing equilibrium potentials, and effects of channel blocking drugs..." For more information see Jeffery L. Ram's Home Page or the Department of Physiology Biopolymer BIOPOLYMER CALCULATIONS BIOPOLYMER CALCULATOR - Schepartz Lab, Department of Chemistry, Yale University "This form can be used to calculate the molecular weight, the extinction coefficient, the concentration, and the melting temperature of a single stranded nucleic acid. Additionally, you can enter a protein sequence, and the form will calculate the molecular weight (using average isotopic mass), extinction coefficient, the concentration, and the formal charge." For more information see Welcome to the Schepartz Lab Botany FOR OVER "50" BOTANY DATABASES & COURSES SEE THE BIOSCIENCE & BIOTECHNOLOGY CENTER: BOTANY SOME EXAMPLES FLOWERING PLANT IDENTIFICATION WORLD WIDE FLOWERING PLANT IDENTIFICATION - R. Phillips, Department of Biology, Colby College Multimedia Interactive Database. "This is a polyclave key that allows you to select from among characteristics available in thespecimen at hand, rather than following a sequence found in a traditional, dichotomous, printed key. It is especially useful if the specimen is fragmentary, as with archaeological or anthropological specimens, in which only part of a plant is represented. This key is world-wide in scope covering all flowering plants." For more information see Biology 211: Flowering Plant Taxonomy or the Department of Botany POLLEN POLLEN WATER CONTENT DETERMINOR - P.D. Pennington, Department of Plant Sciences, University of Oxford For more information see Paul Douglas Pennington's Home Page or the Department of Plant Sciences VASCULAR PLANT DATABASE VASCULAR PLANT FAMILY - G. Carr, Department of Botany, University of Hawaii, Manoa, Manoa, Hawaii Multimedia Databases (Text & Images). "The systematic index follows the classification scheme of Arthur Cronquist (1981)." For more information see Gerald (Gerry) Carr's Home Page or the Department of Botany Databases include Hawaiian Native Plant Genera Flowering Plant Familes (magnolias, lilies, etc.) Non-Flowering Plant Family (cycads, conifers, ferns and fern allies) Buffer BUFFER CALCULATIONS BUFFER CALCULATOR - S. Dawson, University of Nottingham, U.K. "This is a Forms based Buffer Calculator." For more information see Simon Dawson's Home Page BUFFERS FOR pH CONTROL (JAVASCRIPT) - R.J. Beynon, Protein Function Group, University of Manchester Institute of Science & Technology, U.K. Make a Buffer includes: Buffer & Volume; pH & Concentration of buffer species; Ionic Strength; and Temperature. For more information see Rob J. Beynon's Home Page or Protein Function Group ACETATE BUFFER CALCULATIONS ACETATE BUFFER CALCULATOR - S.C. Barton, Department of Chemical Engineering, Columbia University "...calculates the amount of acetic acid and sodium acetate necessary to achieve a buffer at a given pH and strength..." For more information see Tools; Scott Calabrese Barton's Home Page or the Department of Chemical Engineering BUFFER SPECIATION BUFFER SPECIATION CALCULATOR - The Compton Group, Physical & Theoretical Chemistry Laboratory, Oxford University, U.K. "...calculates the concentrations of the differently speciated metal and the pH of the buffer given the initial concentrations of acid, salt and metal ion..." For more information see Data Analysis; The Compton Group or the Physical & Theoretical Chemistry Laboratory CITRIC ACID, SODIUM CITRATE & PHOSAPHATE BUFFER CITRIC BUFFER SOLUTION WIZARD (JAVA APPLET) - Developed by J. Clymer & hosted by BD Biosiences, Becton, Dickinson and Company "... Using the three pK's of citric acid and the pH, the ratio's of each of the citrate pairs is calculated..." For more information see BD Biosiences Discovery Labware: Usefull Tools & Web Gadgets or BD Biosiences Also see Phosphate Buffer Solution Wizard CITRIC BUFFER (JAVA APPLET) - J. Clymer, Cincinnati, Ohio "...calculates the amount of citric acid and sodium citrate necessary to achieve a buffer at a given pH and strength..." For more information see Jeffery Clymer's Home Page Examples of other Buffer Calculators include Phosphate Buffer Calculation I Phosphate Buffer Calculation II Carbohydrates CARBOHYDRATES SEE CHEMICALS & BIOCHEMICALS CARBOHYDRATES Cell Biology ACTIN FILAMENT ACTIN FILAMENT: BUILD YOU OWN (JAVA APPLET) - P. McLaughlin & M. Baird, Structural Biochemistry Group, Institute of Cell and Molecular Biology, University of Edinburgh, U.K. VERY EXTENSIVE. For more information see Sellic Talk or the Structural Biochemistry Group AXON POTENTIAL SIMULATOR AXON POTENTIAL SIMULATOR (JAVA APPLET) - J.L. Ram, Department of Physiology, School of Medicine, Wayne State University, Detroit, Michigan VERY VERY EXTENSIVE. "...a Hodgkin-Huxley membrane potential simulation." "...can be used for simulating action potentials, synaptic potentials and their interactions, current injection, voltage clamping, effects of changing equilibrium potentials, and effects of channel blocking drugs..." For more information see Jeffery L. Ram's Home Page or the Department of Physiology CELL CALCULATIONS CELL CALCULATOR (JAVA APPLET) - S. Weber "get direct cell dimensions or reciprocal cell dimensions" For more information see Java Applets; Steffen Weber's Home Page or JCrystal JCELL (JAVA APPLET) - S. Weber "This applet shall visualize the shape of different unit cells and the relations between directional vectors [uvw] and the normals of planes (hkl). Their directions are identical for the cubic system..." For more information see Java Applets; Steffen Weber's Home Page or JCrystal ELECTROPHYSIOLOGY ELECTROPHYSIOLOGY AND THE MULECULAR BASIS OF EXCITABILITY (JAVA APPLETS) - F. Bezanilla, Department of Physiology, member of Brain Research Institute, Neurosciences IDP and The Ahmanson Laboratory of Neurobiology, David Geffen School of Medicine, UCLA VERY EXTENSIVE. For more information see Francisco Bezanilla's Home Page; Department of Physiology or the David Geffen School of Medicine Some examples from over "7" simulations include Voltage dependent Potassium Channel Sodium Channel Simulation Nerve Simulation MICROTUBULE MICROTUBULE: BUILD A (JAVA APPLET) - P. McLaughlin & M. Baird, Structural Biochemistry Group, Institute of Cell and Molecular Biology, University of Edinburgh, U.K. VERY EXTENSIVE. For more information see Sellic Talk or the Structural Biochemistry Group NERNST/GOLDMAN SIMULATOR THE NERNST/GOLDMAN SIMULATOR (JAVA APPLET) - S. Wright, S. Frank, & R. Gore, Department of Physiology, University of Arizona VERY EXTENSIVE. For more information see Nernst/Goldman Simulator Home Page; Chapter 14: Membrane Potential or the Department of Physiology Centrifuge CENTRIFUGE CALCULATIONS G-FORCE & K-FACTOR CALCULATOR - Jouan Inc. "...g-Force Calculator: is used to quickly determine either Centrifuge Speed, Radius or g-Force..." "...k-Factor Calculator: is used to determine the K-Factors for two different centrifuge configurations..." For more information see Lab Support or Jouan Inc. ROTOR CALCULATOR - CENTRIFUGE - F. Hoedemaeker, X-Ray Crystallography, Ontario Cancer Institute, Princess Margaret Hospital, Toronto, Ontario, Canada For more information see X-Ray Crystallography Chromosome - Human, Animal, etc. FOR DATABASES SEE THE BIOSCIENCE CENTER Concentrations/Solutions VIRTUAL LABORATORY & PROTOCOLS MOLECULAR BIOLOGY PROTOCOLS - CALCULATORS - A. Soldatov, Institute of Gene Biology, Russian ELectronic Academic & Research Network Association (RAS), Moscow, Russia & the Max-Planck-Institut fur Molekulare Genetik, Berlin, Germany VERY VERY VERY EXTENSIVE. Also available in German/Deutsch, Russian & Ukrainian. Includes: "recipes of salt solutions, laboratory buffers, media, antibiotics etc..." For more information see Practical Molecular Biology Some examples of Major Categories with include over "70" Calculators Antibiotics Single component solutions Compound solutions Spectrophotometric measurement of nucleic acids concentrations Estimation of time for bacteria growth Conversion: radioactivity - biological amount of dNTP's VIRTUAL LABORATORY (JAVA VIRTUAL MACHINE - JVM) - D. Yaron, D. Lange, J, Chalecki & S. C. Ulrich, Jr., Department of Chemistry, Carneigie Mellon University "The networked laboratory simulation we are currently developing allows users to select from hundreds of chemical reagents and combine them in any ways they see fit. The chemical solutions are stored and retrieved from a network database that contains cabinets for both course and student solutions..." For more information see Applets; The Irydium Project or the Department of Chemistry DNA AND/OR RNA CONCENTRATION CALCULATIONS DNA CONCENTRATION CALCULATOR - S. Venkataraman, Michigan State University For more information see JavaScript or Sridhar Venkataraman's Home Page RNA CONCENTRATION CALCULATOR - K. Fujiwara, Kawai Laboratory, Department of Industrial Chemistry, Chiba Institute of Technology, Japan "Calculates the concentration of nucleic acids in a sample, being single, double stranded DNA, or RNA." For more information see Kazuya Fujiwara's Home Page SOLUTIONS CALCULATORS CHEMICAL SOLUTIONS CONCENTRATION CALCULATOR - Dundee Scientific Ltd., Dundee, Scotland, U.K. "A chemical calculator for making up solutions..." For more information see WebCalculator List of Calculators or WebCalculator Examples of other Chemical Calculators include Chemical Solutions Mass Calculator Chemical Dilution Calculator MIXING TWO SOLUTIONS - J. Pihkala, Leonardo da Vinci Project, Kokkola Vocational Institute, Kokkola, Finland For more information see Chemistry or the Leonardo da Vinci Project - Teaching Chemistry by Vegetable Oil Theme Examples of other Solutions calculators include Mass % Solution Volume % Solution Dilution Pipeting SOLUTION CONCENTRATION CALCULATOR - G. Warren, Warren Laboratory, School of Biological Sciences, Royal Holloway, University of London, U.K. VERY EXTENSIVE. For more information see Calculations and Conversions; Warren Laboratory; Gareth (Gary) Warren's Home Page or the School of Biological Sciences SOLUTION CONCENTRATION CALCULATOR - D.W. Brooks, Center for Curriculum and Instruction, Teachers College, University of Nebraska VERY EXTENSIVE. Includes: Formula, Solute Molar Mass, Solution Volume, Solution Concentration, Find Mass Solute, Display Recipes, etc. For more information see Interactive Materials; David W. Brooks Curriculum and Instruction Page; David W. Brooks Home Page or the Center for Curriculum and Instruction

DNA FOR DATABASES SEE THE BIOSCIENCE CENTER DNA SEQUENCES DNA APPLET - C. Guda, Joint Center for Structural Genomics, San Diego Supercomputer Center (SDSC), University of California San Diego "...performs some basic operations on DNA sequences..." For more information see Java for Fun or Chittibabu Guda's Home Page PCR PRIMERS ELECTRONIC PCR - National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM) VERY EXTENSIVE. "...Use the Electronic PCR feature to test a DNA sequence for the presence of sequence tagged sites..." For more information see National Center for Biotechnology Information PRIMER 3 (JAVA APPLET) - Whitehead Institute for Biomedical Research, MIT VERY VERY VERY EXTENSIVE. For more information see the Whitehead Institute for Biomedical Research CALCULATE PCR PRIMERS (JAVA APPLET) - C. Guda, Joint Center for Structural Genomics, San Diego Supercomputer Center (SDSC), University of California San Diego "...determines PCR primers based on the parameters provided by the user..." For more information see Java for Fun or Chittibabu Guda's Home Page NETPRIMER: PRIMER DESIGN ANALYSIS (JAVA APPLET) - Premier Biosoft International "...combines the latest primer design algorithms with a web-based interface allowing the user to analyze primers over the Internet..." For more information see NetPrimer Home Page; Intuitive Software for the Molecular Biologist or Premier Biosoft International PCR BOX TITRATION CALCULATOR - Attotron Biosensor Corporation "...determines PCR primers based on the parameters provided by the user..." For more information see Sequence Analysis Software; QuizMaker Suite or Attotron Biosensor Corporation FRAGMENT SIZE DNA FRAGMENT SIZE CALCULATOR - Northwestern University Medical School "...calculate DNA fragment sizes for any gel system that has a logarithmic relationship between molecular weight and distance migrated." For more information see Basic Sciences CONCENTRATIONS DNA CONCENTRATION CALCULATOR - S. Venkataraman, Michigan State University For more information see JavaScript or Sridhar Venkataraman's Home Page CONVERSION DNA AND PROTEIN CONVERSION CALCULATOR - G. Warren, Warren Laboratory, School of Biological Sciences, Royal Holloway, University of London, U.K. VERY EXTENSIVE. For more information see Calculations and Conversions; Warren Laboratory; Gareth (Gary) Warren's Home Page or the School of Biological Sciences LIGATIONS & BLUNT-END LIGATIONS DNA LIGATION CALCULATOR - S. Michnick, Stephen Michnick Laboratory, Université de Montréal, Montréal, Canada For more information see Protocals & Tools or Stephen Michnick Laboratory LIGATOR: BLUNT-END LIGATIONS - CALCULATOR - S. Venkataraman, Michigan State University "...estimates amounts of DNA to be used for a blunt end ligation..." For more information see JavaScript or Sridhar Venkataraman's Home Page Electrophoresis ELECTROPHORESIS ELECTROPHORESIS (JAVA APPLET) - Java programming: K.I. Tchourioukanov; Author: M.W. Davidson, Molecular Expressions: Exploring the World of Optics & Mircroscopy, Florida State University "...explores how macromolecules are separated according to size when direct current is applied to the ends of an electrophoresis gel." For more information see Electricty & Magnetism Interactive Java Tutorials or Molecular Expressions: Exploring the World of Optics & Mircroscopy Some examples of other related applets include Resistance at the Molecular Level Mitosis ELECTROPHORESIS SIMULATION OF DNA ELECTROPHORESIS SIMULATION OF DNA (JAVA APPLET) - P.A. Craig, Department of Chemistry, Rochester Institute of Technology VERY EXTENSIVE. For more information see Electrophoresis Simulation Site or Paul A. Craig's Home Page ELECTROPHORESIS SIMULATION OF PROTEINS ELECTROPHORESIS SIMULATION OF PROTEINS (JAVA APPLET) - P.A. Craig, Department of Chemistry, Rochester Institute of Technology VERY EXTENSIVE. "...simulates the process of electrophoesis on proteins. After separation the applet will plot the result and determine the experimental molecular weight of the unknowns..." For more information see Electrophoresis Simulation Site or Paul A. Craig's Home Page FRAGMENT SIZE FRAGMENT SIZE CALCULATOR (GEL SYSTEM) - Northwestern University Medical School "...calculate unknown sizes for any gel system that has a logarithmic relationship between molecular weight and migration..." For more information see Basic Sciences GEL ELECTROPHORESIS GEL ELECTROPHORESIS SIMULATION (JAVA APPLET) - Original Author: J.Cowan, Revised and modified by W. Christian, Department of Physics, Davidson College, North Carolina For more information see Physlets; WebPhysics or the Department of Physics Genetics FOR DATABASES SEE THE BIOSCIENCE CENTER GENETIC CODE GENETIC CODE: THE CONDON-ANTICONDON RELATIONSHIP - GENETICS CALCULATOR - G. Warren, Warren Laboratory, School of Biological Sciences, Royal Holloway, University of London, U.K. VERY EXTENSIVE. For more information see Calculations and Conversions; Warren Laboratory; Gareth (Gary) Warren's Home Page or the School of Biological Sciences GENETIC ALGORITHMS JAVA GENETIC ALGORITHMS TOOLKIT (GA PLAYGROUND) - A. Dolan VERY EXTENSIVE. Over "20" Applets. For more information see Artifical Life or Ariel Dolan's Home Page GENETICS - HALDANE & KOSAMBI MAPPING FUNCTIONS HALDANE & KOSAMBI MAPPING FUNCTIONS - GENETICS CALCULATOR - G. Warren, Warren Laboratory, School of Biological Sciences, Royal Holloway, University of London, U.K. VERY EXTENSIVE. For more information see Calculations and Conversions; Warren Laboratory; Gareth (Gary) Warren's Home Page or the School of Biological Sciences GENETIC POWER CALCULATIONS GENETIC POWER CALCULATOR - S. Purcell & P. Sham, Statistical Genetics Group, Social, Genetic & Developmental Psychiatry Research Centre (SDGP), King's College, London, U.K. VERY EXTENSIVE. For more information see the Statistical Genetics Group Some examples from over "6" Calculators include TDT for discrete traits Quantitative Case-Control PEACHFACED LOVEBIRD GENETICS CALCULATOR PEACHFACED LOVEBIRD GENETICS CALCULATOR (JAVA APPLET) - African LoveBird Society "...allows you to quickly calculate the possible color combinations that can result from a pairing of any two peachfaced lovebirds..." For more information see LoveBird Genetics or the African LoveBird Society Genetic Mutation MUTATIONAL LOAD CALCULATIONS MUTATIONAL LOAD CALCULATOR - S.J. Freeland, Freeland Bioinformatics Laboratory, Department of Biological Sciences, University of Maryland VERY VERY EXTENSIVE. "This tool measures a genetic code's susceptibility to point mutations." For more information see Genetic Code Evolution Tools; Freeland Bioinformatics Laboratory or the Department of Biological Sciences Examples of related Calculators include Codon Sequence Analyzer Freque Genetics (Population) POPULATION GENETICS CALCULATIONS ASSIGNMENT CALCULATOR - J. Brzustowski, Biological Sciences, University of Alberta, Canada "This calculator takes genotypes of individuals from several populations and determines from which population each individual is most likely to have come, by using the assignment index, the highest probability of an individual's genotype in any of the populations." For more information see Programs or Biological Sciences POPULATION GENETICS - K. Christensen, Division of Genetics and Breeding, Department of Animal Science and Animal Health, The Royal Veterinary and Agricultural University (KVL), Frederiksberg C, Denmark Multimedia Course (Text, Images & Video). For more information see Knud Christensen's Home Page or the Department of Animal Science and Animal Health Some examples from over "12" Applets include Chapter 4: Relationship and inbreeding Chapter 7: Estimation of breeding value Chapter 12: Estimating- and biotechnology and disease resistance Chapter 14: Genetic calculations, applets and other programs POPULATION GENETICS (JAVA APPLETS) - K. Holsinger, Department of Ecology & Evolutionary Biology, University of Connecticut VERY VERY EXTENSIVE. For more information see Kent Holsinger's Home Page or the Department of Ecology & Evolutionary Biology Some examples from over "11" Applets include Wahlund Effect and F-statistics Response to selection in a quantitative trait Natural selection and genetic drift Gene Regulation & Prokaryotes GENE REGULATION & BIOINFORMATICS IN PROKARYOTIC PRODORIC: PROKARYOTIC DATABASE OF GENE REGULATION AND REGULATORY NETWORKS - R. Münch, Technical University Carolo-Wilhelmina, Brunswick, Lower Saxony, Germany Multimedia Database & Tools for Visualization & Analysis (Text, Images, Applets). VERY VERY EXTENSIVE. "The Internet Portal for Gene Regulation and Bioinformatics in Prokaryotes" Includes: "Genes and Operons; Proteins (Transcriptional Regulators); Binding Sites; Alphabetical Regulon List; Matrix and Consensi; Chemical Reaction; Possible Pathways; Regulated Compound..." For more information see Autosharp Pens, Autovisuals Some examples of Tools include Weight Matrix JVirGel Proenomics Tools

Immunology SIMULATIONS LAB WORK - A.J. Cann, Department of Microbiology and Immunology, Leicester University, City of Leicester, U.K. "Real data, real results - online experiments you can perform - right here, right now !" For more information see the Department of Microbiology & Immunology or the Leicester University Examples from over '8' Online Experiments include Antibody-Antigen Interactions Mr Campbell's Kidney: The ELISA (Enzyme Linked ImmunoSorbent Assay) assay OUCHTERLONY ANALYSIS SIMULATOR (JAVA APPLET) - H.R. Gutman & G.A. Gutman, Department of Microbiology and Molecular Genetics, University of California, Irvine (UCI) VERY EXTENSIVE. "Choose either "Antigen" or "Antiserum against:" Select a protein (and a hapten, if desired)..." For more information see Immunology Course or the Department of Microbiology and Molecular Genetics VIRTUAL IMMUNOLOGY (SHOCKWAVE) - Howard Hughes Medical Institute "...This virtual laboratory will demonstrate how such a test, termed an enzyme-linked immunosorbent assay (ELISA), is carried out and some of the key..." For more information see Howard Hughes Medical Institute Metabolic Engineering SIMULATIONS OF METABOLISM METABOLIC ENGINEERING: COMPUTER SIMULATION OF METABOLISM - Web Author: D. Rose, Center for Plant Environmental Stress Physiology, Department of Horticulture and Landscape Architecture, Purdue University VERY VERY EXTENSIVE. Includes Java Script Calculators & Java Applets. " This site describes some simple computer routines that can be used to interpret stable isotope and radioisotope tracer kinetics in terms of metabolic fluxes and compartmentation of pools." For more information see Research Activities; Center for Plant Environmental Stress Physiology or the Department of Horticulture and Landscape Architecture Some examples from over "20" Calculators & Applets include Pulse-Chase Labeling Kinetics Simulator Pulse-Chase Labeling Kinetics Simulator With Compartmentation GS/GOGAT Cycle Simulator (Applet) Radiolabeling Kinetics Simulator Radiolabeling Kinetics Simulator Assuming Fixed Rates of Modeling (Applet) Molar Mass & Molarity MOLAR MASS, MOLAR COVERSION, MOLARITY, SOLUTE MOLAR MASS ETC. MOLARITY CALCULATOR: CREATE AND DILUTE MOLAR SOLUTIONS - H. Motulsky, GraphPad Software, Inc. VERY EXTENSIVE. Calculators include: Mass from volume & concentration; Volume from mass & concentration; Molarity from mass & volume; & Dilute a stock solution. For more information see Chemical and radiochemical calculators; GraphPad QuickCalcs or GraphPad Software MOLAR CONVERSIONS CALCULATOR - J. Glassman, Stanford University VERY EXTENSIVE. Includes: Moles ot Particles; Particles to Moles; Molarity; Molar Mass; Grams to Number of Moles; & much more. For more information see Chemistry Functions or Jon Glassman's Home Page MOLAR MASS AND PERCENT BY MASS CALCULATOR - D. Wookcock, Department of Chemistry, Okanagan University College, B.C., Canada For more information see Molecular Models in .pdb Form or the Department of Chemistry MOLAR MASS AND PERCENT BY MASS CALCULATOR - W. Moshammer, Department of Computer Science, University of Technology in Vienna, Vienna, Austria "Putting in a molecular formula of any type such as K2Cr2O7, CH3CH2COOH, KFe[Fe(CN)6]3, or Na2B4O7.10H20 will result in the molar mass and mass analyses being calculated..." For more information see Java Script or Werner's Secret Place MOLAR MASS CALCULATOR - D. Dice Digipac, Microcomputer Software For more information see Chemical Calculations Other Calculators & Databases include Precentage Composition Calculator Atomic, molecular, and formula masses SOLUTION CONCENTRATION CALCULATOR - D.W. Brooks, Center for Curriculum and Instruction, Teachers College, University of Nebraska VERY VERY EXTENSIVE. Includes: Formula, Solute Molar Mass, Solution Volume, Solution Concentration, Find Mass Solute, Display Recipes, etc. For more information see Interactive Materials; David W. Brooks Curriculum and Instruction Page; David W. Brooks Home Page or the Center for Curriculum and Instruction Molecular Biology PROTOCOLS MOLECULAR BIOLOGY PROTOCOLS - CALCULATORS - A. Soldatov, Institute of Gene Biology, Russian ELectronic Academic & Research Network Association (RAS), Moscow, Russia & the Max-Planck-Institut fur Molekulare Genetik, Berlin, Germany VERY VERY VERY EXTENSIVE. Also available in German/Deutsch, Russian & Ukrainian. Includes: "recipes of salt solutions, laboratory buffers, media, antibiotics etc..." For more information see Practical Molecular Biology Some examples of Major Categories with include over "70" Calculators Antibiotics Single component solutions Compound solutions Spectrophotometric measurement of nucleic acids concentrations Estimation of time for bacteria growth Conversion: radioactivity - biological amount of dNTP's MOLECULAR BIOLOGY TOOLS ANDY'S MOLECULAR BIOLOGY LAB - R. Singh, Department of Molecular Cellular and Developmental Biology, University of Colorado VERY EXTENSIVE. For more information see Ravinder Singh's Home Page or the Department of Molecular Cellular and Developmental Biology Some examples of online Molecular Biology Tools include Tm (melting temperature of dsDNA) calculator 32-P Isotope calculator Calculate Kds from filter binding BIOINFO BANK - BioInfo Bank, Kyushu Institute of Technology, Japan VERY VERY VERY EXTENSIVE. For more information see BioInfo Bank - Old address EBI TOOLS - European Bioinformatics Insitute (EBI), European Molecular Biology Laboratory (EMBL), U.K. VERY VERY VERY EXTENSIVE. For more information see EMBL-EBI Databases & Tools or the European Bionformatics Institute MOLECULAR BIOLOGY TOOLS - ExPASy Molecular Biology Server, Geneva University Hospital and the University of Geneva VERY VERY VERY EXTENSIVE. For more information see ExPASy Molecular Biology Server ONLINE ANALYSIS TOOLS - A.M. Kropinski, Department of Microbiology & Immunology, Queen's University, Kingston, Ontario, Canada VERY VERY EXTENSIVE. "...constructed to permit the novice molecular biologist, with access to the Internet, the easy opportunity to derive a considerable amount of useful information from nucleotide or protein sequence data..." For more information see Andrew M. Kropinski's Home Page; Andrew M. Kropinski's Home Page (Department of Microbiology & Immunology) or the Department of Microbiology & Immunology Molecular Mass MOLECULAR MASS CALCULATIONS CHEMIE.DE MOLECULAR MASS CALCULATOR - Chemie.DE Information Service GmbH, a Life Science Network Division For more information see Chemie DE OMDI MASS CALCULATOR (JAVA APPLET) - Octavian Micro Development Inc. "Lets you calculate the mass of a molecule." For more information see Java Applets; Engineering and Science or Octavian Micro Development Inc. CALCULATE ELEMENTAL COMPOSITION FROM A GIVE MOLECULAR MASS ELEMENTAL COMPOSITION CALCULATOR - J.A. McCloskey, P.F. Crain, & J. Rozenski, Huntsman Cancer Institute, University of Utah "Calculates elemental compositions from a given molecular mass." For more information see the Nucleic Acids Masspec Toolbox or the Huntsman Cancer Institute CALCULATE MOLECULAR MASS & ISOTOPE RATIOS FROM ELEMENTAL COMPOSITIONS MO1E - MOLECULAR MASS CALCULATOR - J.A. McCloskey, P.F. Crain, & J. Rozenski, Huntsman Cancer Institute, University of Utah, University of Utah "Calculates molecular masses and isotope ratios from elemental compositions." For more information see the Nucleic Acids Masspec Toolbox or the Huntsman Cancer Institute FORMULA TO MASS TO FORMULA WELCOME TO THE FORMULA TO MASS TO FORMULA APPLET PAGE - G. Cottenceau, Department of Chemistry, Imperial College of Science, Medicine and Technology, U.K. For more information see Examples of the Application of Java to Chemistry Molecular Weight ATOMIC MASS OF ATOMS AND COMPOUNDS ATOMIC MASS OF ATOMS AND COMPOUNDS CALCULATOR - J. Glassman, Stanford University VERY EXTENSIVE. For more information see Chemistry Functions or Jon Glassman's Home Page MOLECULAR FORMULA FROM A HRMS WEIGHT FIND MOLECULAR FORMULA FROM A HRMS WEIGHT (JAVA APPLET) - J.M. Goodman, Department of Chemistry, Cambridge University For more information see Chemical Calculations; Goodman Group; Jonathan M. Goodman's Home Page; Department of Chemistry or the Cambridge Univerisy Chemical Laboratory MOLECULAR WEIGHTS & CHEMICALS MOLECULAR WEIGHTS & CHEMICAL CALCULATOR - B. Hanson, Department of Chemistry, St. Olaf College, Morthfield, Minnesota VERY VERY EXTENSIVE. For more information see Calculators or Bob Hanson's Home Page MOLECULAR WEIGHT MOLECULAR WEIGHT CALCULATION (JAVA APPLET) - J.M. Goodman, Department of Chemistry, Cambridge University For more information see Chemical Calculations; Goodman Group; Jonathan M. Goodman's Home Page; Department of Chemistry or the Cambridge Univerisy Chemical Laboratory MOLECULAR WEIGHT CALCULATOR (JAVA APPLET) - ChemicalLogic For more information see ChemicalLogic Corporation MOLECULAR WEIGHT CALCULATION - Chemistry Department, Freie Universität Berlin Hypertext. A Searchable Index: "Type in chemical molecular formula"/"Geben Sie eine chemische Summenformel ein". For more information see the Department of Chemistry, Freie Universität Berlin or Fachbereich Chemie, Freie Universität Berlin RNA, DNA, PROTEIN MOLECULAR WEIGHT MOLECULAR WEIGHT CALCULATOR - R. Singh, Department of Molecular Cellular and Developmental Biology, University of Colorado "Enter Sequence (RNA, DNA or Protein) that you want the molecular weight of..." For more information see Andy's Molecular Biology Lab; Ravinder Singh's Home Page or the Department of Molecular Cellular and Developmental Biology PROTEIN MOLECULAR WEIGHT CALCULATOR - S. Venkataraman, Michigan State University For more information see JavaScript or Sridhar Venkataraman's Home Page

Multiple Alignments COLOUR INTERACTIVE EDITOR FOR MULTIPLE ALIGHNMENTS CINEMA: COLOUR INTERACTIVE EDITOR FOR MULTIPLE ALIGHNMENTS - D.J. Parry-Smith, A.W.R. Payne, A.D. Michie & T.K. Attwood and hosted by University of Manchester Bioinformatics Education and Research (UMBER), University of Manchester, U.K. Multimedia Database (Text & Images). VERY VERY EXTENSIVE. "CINEMA allows you to build alignments interactively, either using a free-format Cut and Paste facility to import your own protein or DNA sequences, or by adding sequences directly from the OWL composite database. Alternatively, alignments may be loaded from the PRINTS fingerprint database, and again may be customised by the addition of user-defined or OWL sequences." For more information see UMBER Muscle Contraction MUSCLE CONTRACTION ACTIN FILAMENT: BUILD YOU OWN (JAVA APPLET) - P. McLaughlin & M. Baird, Structural Biochemistry Group, Institute of Cell and Molecular Biology, University of Edinburgh, U.K. VERY EXTENSIVE. For more information see Sellic Talk or the Structural Biochemistry Group Neural Networks & Artifical Life ARTIFICIAL LIFE & NEURAL NETWORKS APPLETS FOR NEURAL NETWORKS AND ARTIFICIAL LIFE - A. Utsugi, Human Informatics Department, National Institute of Bioscience and Human-Technology, Japan Index of Applets, Simulations, & Calculators WW. For more information see Akio Utsugi's Home Page ARTIFICIAL LIFE - D. Griffeath, Mathematics Department, Cornell University For more information see David Griffeath's Home Page Examples of Applets include Greenberg-Hastings Models Life Without Death: Some Elementary Interactions BOIDS MODEL BOIDS MODEL (JAVA APPLET) - C.W. Reynolds, Reynolds Engineering & Design "This is a demonstration of the boids model of bird flocking (and related group motion) " For more information see Sitemap or Reynolds Engineering & Design FLOYS FLOYS: TERRITORIAL ARTIFICAL LIFE FLOCKING JAVA CREATURES (JAVA APPLET) - A. Dolan For more information see Artifical Life or Ariel Dolan's Home Page NEURAL NET CONCEPTS NEURAL NET CONCEPTS (JAVA APPLET) - Computation and Neural Networks Laboratory. Department of Electrical & Computer Engineering, College of Engineering, Wayne State University For more information see Computation and Neural Networks Laboratory Examples from over '20' Applets include Extreme Point Machine (EPM): 2-D 2-Class VersionL 2D Time Dynamical System Nucleic Acids NUCLEIC ACID CALCULATIONS NUCLEIC ACID CALCULATOR - R.P. Grant, Laboratory of Molecular Biology, Cambridge University, U.K. For more information see the Lab Resources: Methods or RPG's MRC Pages NUCLEIC ACIDS MASSPEC TOOLBOX - J.A. McCloskey, P.F. Crain, & J. Rozenski, Huntsman Cancer Institute, University of Utah VERY EXTENSIVE. For more information see the Huntsman Cancer Institute Some examples of online calculators include Mongo Oligo Mass Calculator Elemental Composition Calculator Oligo Composition Calculator Nucleotide Mass NUCLEOTIDE MASS CALCULATIONS NUCLEOTIDE MASS CALCULATOR (DNA & RNA) (JAVA) - R.C. Beavis & D. Fenyñ, PROWL; hosted by the Rockefeller University Multimedia Databases & Tutorials (Text & Images). For more information see Prowl

Oligonucleotide MONGO OLIGO MASS CALCULATOR MONGO OLIGO MASS CALCULATOR - J.A. McCloskey, P.F. Crain, & J. Rozenski, Huntsman Cancer Institute, University of Utah "The ultimate oligonucleotide mass calculator, calculates also electrospray series, CID fragments, endo- and exonuclease fragments..." For more information see the Nucleic Acids Masspec Toolbox or the Huntsman Cancer Institute OLIGONUCLEOTIDE CALCULATIONS OLIGONUCLEOTIDE CALCULATOR - Eugen Buehler, University of Pittsburgh School of Medicine OLIGO CALCULATOR - E. Buehler, Department of Molecular Gnentics & Biochemistry, University of Pittsburgh For more information see Department of Molecular Gnentics & Biochemistry OLIGONUCLEOTIDE PROPERTIES CALCULATIONS OLIGONUCLEOTIDE PROPERTIES CALCULATOR - Q. Cao, Northwestern University Medical School VERY EXTENSIVE. For more information see Basic Sciences OLIGONUCLEOTIDE TM DETERMINATION CALCULATIONS OLIGONUCLEOTIDE TM DETERMINATION: CALCULATOR - Virtual Genome Center, University of Minnesota "These calculations are done essentially as described by Breslauer et al., Proc. Nat. Acad. Sci. 83, 3746-50, 1986." For more information see Virtual Genome Center, University of Minnesota Peptide Mass ACCURATE MASS & PEPTIDE MODIFICATION ACCURATE MASS & PEPTIDE MODIFICATION - A. Bohne-Lang, Molecular Modeling, Central Sectroscopy Department, German Cancer Research Center (DKFZ), Heidelberb, Germany "Help to unravel information encrypted in the deltamass value of accurate peptide masses. Deltamass is the post-decimal-point part of the accurate mass..." For more information see the Andreas Bohne-Lang's Home Page; Central Sectroscopy Department - Molecular Modeling or PEPTIDE MASS CACLULATIONS PEPTIDE MASS CACLULATOR - R.C. Beavis & hosted by Peptide Protein Research Ltd. For more information see Peptide Synthesis PEPTIDE MASS CACLULATOR - J. Rozenski, Bio Analytical Mass Spectrometry Facility, Rega Institute for Medical Research, Belgium For more information see Mass Calculators or the Bio Analytical Mass Spectrometry Facility PEPTIDE MASS - ExPASy Molecular Biology Server, Geneva University Hospital and the University of Geneva "Calculate masses of peptides and their posttranslational modifications for a SWISS-PROT entry or for a user sequence." For more information see ExPASy Tools Menu or ExPASy Molecular Biology Server Proteins PROTEIN TOOLS EXPASY PROTEOMICS TOOLS - ExPASy Molecular Biology Server, Geneva University Hospital and the University of Geneva VERY VERY VERY EXTENSIVE. Tools Include: "Protein identification and characterization; DNA -> Protein; Similarity searches; Pattern and profile searches; Post-translational modification prediction; Primary structure analysis; Secondary structure predictiong; Tertiary structure; Transmembrane regions detection; and Sequence alignment..." For more information see ExPASy Molecular Biology Server BRADFORD TEST BY REGRESSION ANALYSIS BRADFORD TEST BY REGRESSION ANALYSIS - CALCULATOR - S. Venkataraman, Michigan State University "...evaluates protein concentrations based on OD595..." For more information see JavaScript or Sridhar Venkataraman's Home Page DNA AND PROTEIN CONVERSION DNA AND PROTEIN CONVERSION CALCULATOR - G. Warren, Warren Laboratory, School of Biological Sciences, Royal Holloway, University of London, U.K. VERY EXTENSIVE. For more information see Calculations and Conversions; Warren Laboratory; Gareth (Gary) Warren's Home Page or the School of Biological Sciences PROTEIN MOLECULAR WEIGHT CALCULATIONS PROTEIN MOLECULAR WEIGHT CALCULATOR - S. Venkataraman, Michigan State University For more information see JavaScript or Sridhar Venkataraman's Home Page Protein - Calcium Binding Proteins PER RESIDUE SOLVENT ACCESSIBLE SURFACE CACLULATIONS PER RESIDUE SOLVENT ACCESSIBLE SURFACE CALCULATOR - Developed by M. Nelson, The EF-Hand Calcium Binding Proteins Data Library; Walter Chazin's Laboratory, Vanderbilt University "Calculate the per residue solvent accessible surface area for a residue in one of the structures of calbindin D(9k), calmodulin, or troponin C, and simultaneously for the residue's homologs in the other proteins." For more information see The CABP Data Library (Analytical Tools); The EF-Hand Calcium Binding Proteins Data Library or the Program in Structural Biology HOMOLOG FINDER HOMOLOG FINDER - Developed by M. Nelson, The EF-Hand Calcium Binding Proteins Data Library; Walter Chazin's Laboratory, Vanderbilt University "Enter a residue number and choose an EF-hand CaBP, and find the homolgous residues in any other proteins in the main alignment" For more information see The CABP Data Library (Analytical Tools); The EF-Hand Calcium Binding Proteins Data Library or the Program in Structural Biology Protein Folding PROTEIN & MACROMOLECULES MOVEMENTS/MOTIONS - MOVIES, SIMULATIONS MOLECULAR MOVEMENTS DATABASE - N. Echols, Bioinformatics Web Server, Department of Molecular Biophysics and Biochemistry, Yale University Multimedia (Text, Images & Movies). This database describes the motions that occur in proteins and other macromolecules (such as RNA). Associated with it are a variety of free software tools for structural analysis." For more information see the Bioinformatics Web Server Examples from over '100' Molecular Movements currently online include Motion in HIV-1 protease [hivprot] Motion in Lactate Dehydrogenase (LDH) [ldh] Other online Databases include Movie Gallery of Macromolecular Motions [GdmCl] AND [UREA] CALCULATIONS [GdmCl] AND [UREA] CALCULATOR - T. Sosnick, Sosnick Group, Folding & Design, Department of Biochemistry & Molecular Biology, University of Chicago For more information see Sosnick Group or the Department of Biochemistry & Molecular Biology [GuHCl] AND [UREA] CALCULATIONS [GuHCl] AND [UREA] CALCULATOR - D. Baker, The Baker Laboratory (Protein Folding), Department of Biochemistry, University of Washington For more information see The Baker Laboratory or the Department of Biochemistry Protein Crystallography CRYSTALLOGRAPHIC TOOLS QUASICRYSTAL JAVA APPLETS - S. Weber VERY VERY EXTENSIVE. For more information see Steffen Weber's Home Page or JCrystal Protein Identification PROTEIN IDENTIFICATION TOOLS EXPASY PROTEOMICS TOOLS - PROTEIN IDENTIFICATION & CHARACTERIZATION - ExPASy Molecular Biology Server, Geneva University Hospital and the University of Geneva VERY VERY EXTENSIVE. For more information see ExPASy Molecular Biology Server PEPFRAG CALCULATIONS PEPFRAG CALCULATOR (JAVA) - R.C. Beavis & D. Fenyñ, PROWL; hosted by the Rockefeller University "Protein identification by comparison of the fragmentation pattern of one or two peptides to a database." For more information see Protein Identification or Prowl PROTEIN PROSPECTOR PROTEIN PROSPECTOR - K. Clauser & P. Baker, Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, School of Pharmacy, UCSF VERY VERY VERY EXTENSIVE. For more information see Mass Spectrometry Facility or the Department of Pharmaceutical Chemistry Example of Peptide/Protein Calculators include MS-Digest MS-Product TRANSLATION TOOLS TRANSLATE TOOL - ExPASy Molecular Biology Server, Geneva University Hospital and the University of Geneva "Translate is a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence." For more information see ExPASy Tools Menu or ExPASy Molecular Biology Server Protein Structure PROTEIN STRUCTURE VIEWER PROTEIN STRUCTURE VIEWER - U.K. Human Genome Mapping Project Resource Centre Index of protein structure viewer and display sites. For more information see GenomeWeb Protein Translation PROTEIN TRANSCRIPTION AND TRANSLATION TOOLS TRANSCRIPTION AND TRANSLATION TOOL - Attotron Biosensor Corporation "...Converts DNA to RNA to protein..." For more information see Sequence Analysis Software; QuizMaker Suite or Attotron Biosensor Corporation RNA FOR DATABASES SEE THE BIOSCIENCE CENTER RNA SECONDARY STRUCTURE VIEWER RNA SECONDARY STRUCTURE VIEWER APPLET (JAVA APPLET) - R.M. Felciano & R. Altman, Helix Group, Stanford Section on Medical Informatics, Stanford Universtiy "This page demonstrates a Java applet for viewing RNA secondary structures and linking to multiple computational backends." For more information see Helix Group, Stanford Universtiy Sequencing FOR DATABASES SEE THE BIOSCIENCE CENTER AMINO ACID COMPOSITION AMINO ACID COMPOSITION - Pôle Bio-Informatique Lyannais (PBIL), Laboratoire de Biométrie, Biologie Evolutive (Biometry and Evolutionary Biology), Institut de biologie et Chime des Protéines (Institute of Biology and Chemistry of Proteins), Lyon, France "...a simple tool giving you the amino-acid composition of your protein, its mass (Da) and the theoretical molecular epsilon at 280nm..." For more information see Pôle Bio-Informatique Lyannais (PBIL); Laboratoire de Biométrie, Biologie Evolutive or the Institut de biologie et Chime des Protéines PROTEIN PROSPECTOR PROTEIN PROSPECTOR - K. Clauser & P. Baker, Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, School of Pharmacy, UCSF VERY VERY EXTENSIVE. For more information see Mass Spectrometry Facility or the Department of Pharmaceutical Chemistry Example of Sequence Calculators include MS-Fit MS-Tag SEQUENCE ANALYSIS SEQUENCE ANALYSIS - CALCULATORS - Attotron Biosensor Corporation For more information see Attotron Biosensor Corporation Some example of Sequence Calculators include Transcription and Translation Tool Homologous Recombiner Sequence Pattern Finder SEQUENCE RETRIEVAL SYSTEM - European Molecular Biology Laboratory (EMBL) VERY VERY EXTENSIVE. For more information see Tools or European Molecular Biology Laboratory (EMBL)

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