MARTINDALE'S CALCULATORS ON-LINE CENTER BIOSCIENCE & BIOTECHNOLOGY (Calculators, Applets, Spreadsheets, and where Applicable includes: Courses, Manuals, Handbooks, Simulations, Animations, Videos, etc.)

US/Pacific: Tuesday, January 6, 2009 Sydney, Australia: Wednesday, January 7, 2009 File Download Time Calculator Author, E-Mail, Privacy Policy & Disclaimer Currently the Calculators On-Line Center contains over "23,635" Calculators & Spreadsheets, over "3,475" Courses, Lectures, Manuals, Handbooks, & "1,000's" of Movies, Videos, Simulations & Animations

BIOSCIENCE & BIOTECHNOLOGY Analytical Ultracentrifugation ~ Axon Potential Botany ~ Buffers ~ Carbohydrates ~ Cell Biology Centrifuge ~ Cognition Concentrations & Solutions ~ DNA & PCR Primers ~ Electrophoresis ~ Genetics Genetics (Population) ~ Gene Regulation & Prokaryotes Glycoscience ~ Immunology ~ Metabolic Engineering Molecular Biology & Bioinformatics Molecular Mass, Molar Mass, Exact Mass, Molarity, Elemental Composition, Isotope Ratios, etc. Molecular Weight ~ Multiple Alignments Neural Networks & Artificial Life Nucleic Acids & Nucleotide Mass Oligonucleotide ~ Peptide Mass ~ Proteins ~ Protein - Calcium Binding Protein Crystallography ~ Protein Folding ~ Protein Identification Protein Translation Calculators On-Line Center

Analytical Ultracentrifugation ANALYTICAL ULTRACENTRIFUGATION CALCULATORS & SOFTWARE SEDFIT: ANALYTICAL ULTRACENTRIFUGATION (AUC) DIRECT BOUNDARY MODELING - Author: P. Schuck VERY VERY VERY...EXTENSIVE. SEDFIT features include "...analysis of data from: sedimentation velocity, dynamic light scattering, and sedimentation equilibrium. Sedimentation velocity data can be acquired using absorbance or interference optics, in conventional loading configuration or synthetic boundary, analytical zone centrifugation,..." SEDFIT Calculators include: "...Axial and Frictional Coefficient Ratios Calculator; Shapes from Frictional Ratio Calculator; Sedimentation Coefficient for Spherical Particles Calculator; Molar Mass for a Particle at given s-value Calculator; Faxén Solution Calculator; Radial Dilution Calculator; etc. SEDPHAT - Author: P. Schuck VERY VERY VERY...EXTENSIVE. SEDPHAT "...is an extended version of Sedfit for the global analysis of several sedimentation velocity, sedimentation equilibrium, and/or dynamic light scattering experiments. At the same time, it is a stand-alone sedimentation equilibrium analysis software. Further, isotherms of weight-average sedimentation coefficients or weight-average molar mass values can be..." WINDCDT; WINNONLIN; WINMATCH; WINREEDIT; HETEROANALYSIS - National Analytical Ultracentrifugation Facility (NAUF) VERY VERY VERY...EXTENSIVE. Analytical Ultracentrifugation "...software for the manipulation and analysis of ultracentrifugation data..." For more information see the National Analytical Ultracentrifugation Facility (NAUF) Axon Potential AXON POTENTIAL CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS 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." Axon Potential Simulator "...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 THE HODGKIN-HUXLEY MODEL (JAVA APPLET) - Elizabeth Cherry & Flavio Fento, The Virtual Heart, Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University VERY EXTENSIVE. Hodgkin-Huxley Simulation "...solves the equations and can plot all four variables of the model simultaneously. The time of integration is initially set to 40 ms but can be varied easily by changing the time value. Other parameters that can be changed are the time at which..." For more information see The Virtual Heart SIMULATING A HODGKIN-HUXLEY (JAVA APPLET) - Laboratory of Computational Neuroscience, School of Computer and Communication Sciences, EDFL, Switzerland VERY EXTENSIVE. Hodgkin-Huxley Calculator INPUT Values include: "...Cell Diameter; G_Na; G_K; Na_i; K_i; Current Clamp or Voltage Clamp; etc..." For more information see Neural Java or the Laboratory of Computational Neuroscience Botany BOTANY CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS FLOWERING PLANT IDENTIFICATION CALCULATORS & APPLETS WORLD WIDE FLOWERING PLANT IDENTIFICATION - R. Phillips, Department of Biology, Colby College Multimedia Interactive Flowering Plant Database (Text & Images). Flowering Plant Identification "...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 BOTANY CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PLANT PATTERN FORMATION CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PHYLLOTAXIS APPLETS - P. Atela-Cortés & C. Golé, Department of Mathematics, Smith College VERY VERY EXTENSIVE. Phyllotaxis "...An Interactive site for the Mathematical Study of Plant Pattern Formation..." For more information see Introduction to Phyllotaxis; Pau Atela-Cortés' Home Page; Christophe Golé's Home Page or the Department of Mathematics Some examples Plant Pattern Formation Calculators & Applets include Cylinder Lattices Applet Cylinder Lattices Applet "...shows all the possible (half) cylindrical lattices..." Spiral Lattices Applet Spiral Lattices Applet "...enables the exploration of all possible spiral lattices and their organization according to their divergence angles, expansion rate, and parastichy numbers..." Dynamical Model Applet (Centric Representation) Dynamical Model Applet "...shows a model of primordia growth (represented by dots) at the apical meristem of a plant. The model is a dynamical system which implements Hofmeister's hypotheses: primordia form periodically, once formed..." Buffer BIOLOGICAL BUFFER CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS BIOLOGICAL BUFFER CALCULATOR - Sigma-Aldrich VERY VERY EXTENSIVE. Select from Buffer List "...ACES; ADA; Ammonim Tartrate; AMP; AMPD; BES; BES Sodium Salts; BIS-TRIS; Boric Acid; CABS; CAPSO; Citric Acid; DIPSO; DIPSO Sodium Salts; Ethanolamne; Glycolic Acid; HPEBS; HEPES; IMDAZOLE; etc..." For more information see Biological Buffers or Sigma-Aldrich BUFFER CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS BUFFERS FOR pH CONTROL - R. Beynon, Proteomics and Functional Genomics Research Group (PFG), Department of Veterinary Preclinical Sciences, Faculty of Veterinary Science, University of Liverpool, U.K. VERY VERY EXTENSIVE. Buffers for pH Control "...A recipe calculator for thermodynamically correct buffers for pH control..." "...Choose the buffer species you want to use, and enter parameters for volume, pH, and concentration of buffer species. Then, include the option to modify the ionic strength by addition of neutral salt..." Buffers for pH Control INPUT Values include: Buffer Species "...Maleate; Phosphate; Formate; Benzoate; Acetate; Pyridine; Bis-tris; ADA; PIPES; ACES; Phosphate; Tricine; etc..." Volume; pH; Concentration; Control of Ionic Strength; Ionic Strength; Control Ionic Strength; Prepare Buffer at Tempterature; Use Buffer at Temperature. For more information see Rob Beynon's Home Page or the Proteomics and Functional Genomics Research Group (PFG) CITRIC ACID CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS SODIUM CITRATE CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PHOSAPHATE BUFFER CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS CITRIC BUFFER - J. Clymer, Cincinnati, Ohio Citric Buffer Calculator "...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 Phosphate Buffer Calculators include Phosphate Buffer Calculator I Phosphate Buffer Calculator I "...calculates the amount of monosodium phosphate and trisodium phosphate necessary to achieve a buffer at a given pH and buffer strength..." Phosphate Buffer Calculator II Phosphate Buffer Calculator II "...calculates the amount of monosodium phosphate and disodium phosphate necessary to achieve a buffer at a given pH and buffer strength..." Carbohydrates CARBOHYDRATES RELATED CENTER FOR CARBOHYDRATES SEE THE CHEMICALS & BIOCHEMICALS CENTER: CARBOHYDRATES Cell Biology CELL CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS CELL CALCULATOR (JAVA APPLET) - S. Weber VERY EXTENSIVE. Cell Calculator allows you to "...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 VERY EXTENSIVE. JCell Structure Display Calculator will "...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 CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS ELECTROPHYSIOLOGY AND THE MULECULAR BASIS OF EXCITABILITY (JAVA APPLETS) - F. Bezanilla, Department of Physiology, Member of the Brain Research Institute, Neurosciences IDP and The Ahmanson Laboratory of Neurobiology, David Geffen School of Medicine, UCLA Multimedia Electrophysiology Teaching Modules, Laboratory Manual, Calculators, etc. (Text & Images). VERY VERY VERY...EXTENSIVE. Examples of "Electrophysiology and The Molecular Basis of Excitability" includes: The Nerve Impulse "...a brief Textbook that covers the basics of the initiation and propagation of the nerve impulse using equivalent circuits..." Nerve Impulse Laboratory Manual "...Experiments using the NERVE program..." "...These experiments are based upon the squid giant axon, however, the principles that you learn here can be directly applied to action potentials in the mammalian nervous system..." Simulations of Ion Channels and Excitable Membranes include: "...Diffusion Simulation; Membrane Simulation; Nerve Simulation; Cable Properties of the Axon Simulation; Voltage dependent K Channel Simulation; Sodium Channel Simulation; Equivalent Circuit of The Axon Simulation; Model of Shaker K channel gating..." For more information see Francisco Bezanilla's Home Page; Department of Physiology or the David Geffen School of Medicine Some examples from over "7" Electrophysiology Simulations: Simulations of Ion Channels and Excitable Membranes include Equivalent Circuit of The Axon Equivalent Circuit of The Axon Simulation "...shows the equivalent circuit of the membrane capacitance and the three main conductances of the squid giant axon. The conductances are shown as variable resistor, the reversal potentials..." Sodium Channel Simulation Sodium Channel Simulation "...depicts a very simplified and idealized cartoon of three of the four S4 segments and the inactivating particle of the sodium channel..." Nerve Simulation Nerve Simulation "...simulates the generation and propagation of the action potential by solving the Hodgkin and Huxley (HH) model for the space-clamped..." CELL ELECTROPHYSIOLOGY SIMULATION ENVIRONMENT (CESE) - Sergey Missan, Department of Physiology and Biophysics, Faculty of Medicine, Dalhousie University, Canada VERY VERY VERY...EXTENSIVE. Cell Electrophysiology Simulation Environment (CESE) "...is a comprehensive framework specifically designed to perform computational electrophysiological simulations, for example, simulations of cardiac myocyte electrical activity. CESE is useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations..." For more information see Sergey Missan's Home Page or the Department of Physiology and Biophysics

Centrifuge CENTRIFUGE CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS CENTRIFUGE G-FORCE CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS CENTRIFUGE K-FACTOR CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS CENTRIFUGE ROTOR CALCULATOR - Beckman Coulter, Inc. VERY EXTENSIVE. Centrifuge Rotor Calculator INPUT Values include: "...Motor Type; Radius Minimum & Maximum; Maximum Rotor Speed; etc..." For more information see Centrifugation Lab Resources; Lab Resources or Beckman Coulter, Inc. CENTRIFUGATION ROTOR CALCULATOR & ROTOR COMPARISON CALCULATOR - Chang Bioscience, Inc. VERY EXTENSIVE. Centrifugation Rotor Calculator INPUT Values include: "...Select a Brand; Radius Minimum & Maximum; Maximum Rotor Speed; etc..." For more information see Bioinformatics Tools and Resources for Biomedical Scientists and Students or Chang Bioscience, Inc. G-FORCE CALCULATOR - CENTRIFUGE - T.J. Nelson Centrifuge G-Force Calculator INPUT Values include: "...RPM or G-Force; Rotor Type..." For more information see T.J. Nelson's Home Page ROTOR CALCULATOR - CENTRIFUGE - F. Hoedemaeker, X-Ray Crystallography, Ontario Cancer Institute, Princess Margaret Hospital, Toronto, Ontario, Canada Centrifuge Rotor Calculator INPUT Values include: "...Rotor Type; Radius Minimum & Maximum; Maximum Rotor Speed; Calculate for either RPM, RCF Average, RCF Maximum, or k-Factor..." For more information see X-Ray Crystallography RUN TIME CONVERSION USING K-FACTORS - Beckman Coulter, Inc. VERY EXTENSIVE. Centrifuge Run Time Conversion Using k-Factors Calculator INPUT Values include: "...Select Rotor 1; Select Rotor 2; Enter Run Speed for Both; Enter Run Time for Both; Enter k-Factor for Both..." For more information see Centrifugation Lab Resources; Lab Resources or Beckman Coulter, Inc. Cognition COGNITION CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS COGNITIVE CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS LNSC CASCADE CORRELATION SIMULATOR APPLET - F. Dandurand, F. Rivest, M. Stolle & T. Shultz, Laboratory for Natural and Simulated Cognition, McGill University, Canada Cascade-correlation Simulator is "...a program that produces an output-activation diagram for a network with two continuous INPUT Values, a single binary output unit, and random connection weights..." For more information see the Laboratory for Natural and Simulated Cognition MODELS OF MEMORY (JAVA APPLETS) - Ian Neath, Department of Psychology, Memorial University of Newfoundland Multimedia Psychology Models, Models of Memory & Psychology Calculators (Text & Images). VERY VERY VERY...EXTENSIVE. Models of Memory "...If you wish to conduct simulations that will be reported in scientific journals or at professional conferences, you should program your own implementation and should test that version against all relevant published simulations..." For more information see Ian Neath's Home Page or the Department of Psychology Some examples from over "17" Memory Models & Psychology Calculators include The Brown & Hulme Model (Brown & Hulme, 1995) Brown & Hulme Model "...The purpose of the Brown and Hulme (1995) model was to show that item length (or word length) effects could be obtained in a model that does not include any rehearsal..." Positional Distinctiveness (Nairne et al., 1997) Positional Distinctiveness Model "...The basic idea was to see whether Estes' (1972) perturbation model could serve as the cause of distinctiveness. An item's position is encoded accurately, but then perturbs (or drifts) in psychological space..." Johnson's Distinctiveness Model (Johnson, 1991) Johnson's Distinctiveness Model "...Johnson (1991) proposed a distinctiveness model of serial learning. This simulation implements his model...." SIMPLE: Absolute Identification (Neath, Brown, McCormack, Chater, & Freeman, 2006) Scale Invariant Memory and Perceptual Learning (SIMPLE) Model "...assumes that the memory representation is a log transform of the physical item. In this version, however, we use a power function such that...." Recognition Memory Simulation Recognition Memory Simulation includes "...Signal Detection Theory; Non-Parametric Analog; Two-High Threshold Model...." THE HEURISTICA APPLET - Center for Adaptive Behavior and Cognition, Max Planck Institute for Human Development, Berlin, Germany VERY EXTENSIVE. Heuristic Calculator "...is an algorithm which will make decisions based on data. In this case, the heuristics are given data which consist of a number of objects, and some information about the objects in terms of binary cues..." For more information see Simple Heuristics That Make Us Smart Concentrations - Solutions CHEMICAL SOLUTIONS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS BIOCHEMICAL SOLUTIONS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS VIRTUAL LABORATORIES CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PROTOCOLS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS 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. Available in English German/Deutsch, Russian & Ukrainian. Molecular Biology Calculators Subject Categories include: "...Salt Solution Calculators; Laboratory Buffer Calculators; Single Component Solution Calculators; Compound Solution Calculators; Antibiotic Solution Calculators; etc..." For more information see Practical Molecular Biology Some examples from over "100" Molecular Biology Protocols Calculators Antibiotic Solution Calculators Antibiotic Solution Calculators include: "...Working Concentrations and Stock Solutions Calculator; Preparation of Stock Solutions for Ampicillin Calculator; Preparation of Stock Solutions for Carbenicillin Calculator; Preparation of Stock Solutions for Chloramphenicol Calculator; etc.." Single Component Solutions Calculators Single Component Solutions Calculators include: "...Organic Substances Calculators include: ATP Calculator; Betaine Calculator; EDTA Calculator; EtBr Calculator; Gelatin Calculator; HEPES Calculator; PEGV; Sucrose Calculator; etc. Acids and Alkalis Calculators; Detergents Calculator; Organic Solvents Calculators; etc..." Compound Solutions Calculators Compound Solutions Calculators include: "...Electrophoresis Buffer Calculator; Loading Buffer Calculator; Bacteriophage Lambda Buffer Calculator; Denaturation Buffer Calculator; Neutraliszation Buffer Calculator; Plasmid Solution Calculator; Oligonucleotide Gel Staining Mix Calculator; etc..." Spectrophotometric Measurement of Nucleic Acids Concentrations Calculator Spectrophotometric Measurement of Nucleic Acids Concentrations Calculator "...calculates the concentration of nucleic acids according to their optical density: DNA, RNA, Oligonucleotides,..." Estimation of Time for Bacteria Growth Calculator Estimation of Time for Bacteria Growth Calculator: "...This is important for the preparation of chemical- or electro-competent cells and protein expression. The program may be used also for other organisms in the logarithmic stage of growth..." PCR Optimization Calculator PCR Optimization Calculator "...helps to evaluate the quantity of primers and nucleotides for optimal PCR reaction and the necessary number of cycles..." Radioactivity to Biological Amount of dNTPs Calculator Radioactivity to Biological Amount of dNTPs Calculator calculates the "...weight of particular amount of radioactive dNTPs..." VIRTUAL LABORATORY (JAVA APPLET) - The Chemistry Collective & the Department of Chemistry, Carneigie Mellon University VERY VERY VERY...EXTENSIVE. Virtual Lab Simulation "...allows students to select from hundreds of standard reagents and manipulate them in a manner that resembles that of a real lab. It allows students to design and perform diverse experiments in acid-base chemistry, thermochemistry, solubility, and redox chemistry..." For more information see Applets; The Chemistry Collective or the Department of Chemistry DNA CONCENTRATION CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS RNA CONCENTRATION CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS DNA CONCENTRATION CALCULATOR - S. Venkataraman, Michigan State University DNA Concentration Calculator INPUT Values include: "...Volume of BMB marker3; Mol Wt of matching DNA band from BMB marker3; Volume of Test DNA loaded (uL);..." For more information see JavaScript or Sridhar Venkataraman's Home Page

DNA & PCR Primers PCR CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PCR PRIMER CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS ELECTRONIC PCR (FORWARD E-PCR & REVERSE E-PCR) - National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), NIH VERY VERY VERY...EXTENSIVE. Electronic PCR (e-PCR) "...is a computational procedure that is used to identify sequence tagged sites (STSs), within DNA sequences. e-PCR looks for potential STSs in DNA sequences by searching for subsequences that closely match the PCR primers and have the correct order, orientation, and spacing that could represent the PCR primers used to generate known STS's..." For more information see National Center for Biotechnology Information PRIMER 3: PICK PRIMERS FROM A DNA SEQUENCE (JAVA APPLET) - S. Rozen & H. Skaletsky, Whitehead Institute for Biomedical Research, MIT VERY VERY VERY...EXTENSIVE. Primer3 "...is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers..." For more information see Steve Rozen's Home Page or the Whitehead Institute for Biomedical Research NETPRIMER: PRIMER DESIGN ANALYSIS (JAVA APPLET) - Premier Biosoft International VERY VERY EXTENSIVE. NetPrimer "...combines the latest primer design algorithms with a web-based interface allowing the user to analyze primers over the Internet..." For more information see Primer Premier Downloads; NetPrimer Home Page or Premier Biosoft International PCR BOX TITRATION CALCULATOR - Attotron Biosensor Corporation PCR Box Titration Calculator "...calculates the amounts of various ingredients needed to do two-dimensional box titrations of various reactants in polmerase chain reactions..." For more information see Sequence Analysis Software; QuizMaker Suite or Attotron Biosensor Corporation DNA FRAGMENT SIZE CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS DNA FRAGMENT SIZE CALCULATOR - Northwestern University Medical School DNA Fragment Size Calculator "...calculates DNA fragment sizes for any gel system that has a logarithmic relationship between molecular weight and distance migrated..." For more information see Basic Sciences DNA CONCENTRATION CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS DNA CONCENTRATION CALCULATOR - S. Venkataraman, Michigan State University DNA Concentration Calculator INPUT Values include: "...Volume of BMB marker3; Mol Wt of matching DNA band from BMB marker3; Volume of Test DNA loaded (uL);..." For more information see JavaScript or Sridhar Venkataraman's Home Page DNA LIGATION CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS LIGATOR: BLUNT-END LIGATIONS - CALCULATOR - S. Venkataraman, Michigan State University VERY VERY EXTENSIVE. Ligator Calculator "...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 CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS CAPILARY ELECTROPHORESIS CALCULATOR - Beckman Coulter, Inc. VERY VERY EXTENSIVE. Capilary Electrophoresis Calculator INPUT Values include: "...System Type; Capillary Dimensions; Temperature; Pressure; Time;..." Capilary Electrophoresis Calculator OUTPUT Values include: "...Hydrodynamic Injection; Capillary Volume; Capillary Volume to Window; Injection Plug Length; Plug Percentage Length to Window; Capillary Volumes Replaced; Seconds to replace 1 volume; Injection Pressure-seconds; Relative Viscosity..." For more information see Introduction to Capillary Electrophoresis; Capillary Electrophoresis (CE) or Beckman Coulter, Inc. ELECTROPHORESIS (JAVA APPLET) - Java programming: K.I. Tchourioukanov; Author: M.W. Davidson, Molecular Expressions: Exploring the World of Optics & Mircroscopy, Florida State University Electrophoresis Applet "...explores how macromolecules are separated according to size when direct current is applied to the ends of an electrophoresis gel..." For more information see Electricity & Magnetism Interactive Java Tutorials or Molecular Expressions: Exploring the World of Optics & Mircroscopy Some examples of other related Electrophoresis Calculators & Applets include Resistance at the Molecular Level Mitosis CHEMISTRY BASED SIMULATIONS: MOVIES & ANIMATIONS (FLASH, QUICKTIME & REALPLAYER) - T.G. Chasteen, Department of Chemistry, Sam Houston State University, Texas Multimedia Chemistry Laboratory Demonstrations & Experiments Teaching Modules (Text, Images, Videos/Movies & Audio/Sound). VERY VERY VERY...EXTENSIVE. Chemistry Laboratory Video Demonstrations & Experiments "...These animations support the teaching of concepts in chemistry in freshman through graduate level courses..." Subject Categories of Chemistry Laboratory Video Demonstrations & Experiments include: "...Electrophoresis Videos & Animations; Gas Chromatography Videos & Animations; Chromatography Videos & Animations; Chemiluminescence Videos & Animations; Mass Spectrometry Videos & Animations; X-ray Absorption Spectroscopy Videos & Animations; HPLC Videos & Animations; Spectrophotometers Videos & Animations; etc..." For more information see Analytical Environmental Chemistry or Department of Chemistry Some examples of Electrophoresis Videos & Animations include Capillary Electrophoresis Injection Evaluation Videos & Animations Gel Electrophoresis Videos & Animations Capillary Electrophoresis Videos & Animations Modes of Capillary Electrophoresis Videos & Animations ELECTROPHORESIS SIMULATION OF DNA - CALCULATORS & APPLETS ELECTROPHORESIS SIMULATION OF DNA (JAVA APPLET) - P.A. Craig & D. Mix, Department of Chemistry, Rochester Institute of Technology VERY EXTENSIVE. For more information see Electrophoresis Simulation Site or Paul A. Craig's Home Page GEL ELECTROPHORESIS SIMULATION (JAVA APPLET) - R. Russell, MSU's Virtual University, Michigan State University VERY EXTENSIVE. Gel Electrophoresis Simulation "...is used to analyze DNA or proteins. After using enzymes to cut the long DNA or protein strands, the DNA or protein. sample is placed in a "well" along the top of the jello-like gel. Next, current is applied to the gel..." For more information see Randy Russell's Interactive Portfolio; Randy Russell's Home Page or MSU's Virtual University DNA DISCOVERY MODULES (SHOCKWAVE) - The MyDNA Project, Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst VERY EXTENSIVE. For more information see the Department of Biochemistry and Molecular Biology Some examples DNA Discovery Modules include Module 2: Sorting DNA Molecules Module 3: Comparing Different Samples of DNA - Comparing DNA Samples on Agarose Gels ELECTROPHORESIS SIMULATION OF PROTEINS ELECTROPHORESIS SIMULATION OF PROTEINS (JAVA APPLET) - P.A. Craig & D. Mix, Department of Chemistry, Rochester Institute of Technology VERY EXTENSIVE. Electrophoresis Applet "...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 CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS FRAGMENT SIZE CALCULATOR (GEL SYSTEM) - Northwestern University Medical School Fragment Size Calculator "...calculates unknown sizes for any gel system that has a logarithmic relationship between molecular weight and migration..." For more information see Basic Sciences GEL ELECTROPHORESIS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS 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 SODIUM DODECY1 SULFATE POLYACRYLAMIDE GEL ELECTROPHORESIS CALCULATOR (SDS PAGE CALCULATOR) - Chang Bioscience, Inc. VERY EXTENSIVE. Gel Electrophoresis Calculator INPUT Values include: "...Gel percentage; 30% Polyacrylamide; 10% Ammonium persulfate; 10% SD; etc..." For more information see Bioinformatics Tools and Resources for Biomedical Scientists and Students or Chang Bioscience, Inc.

Genetics GENETICS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS GENETIC CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS GENETIC COURSES WITH CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS A TUTORIAL ON THE RELATIONSHIP BETWEEN CHROMOMSOME MOVEMENTS IN MEIOSIS AND THE SEGREGATION OF ALLELES IN MEIOSIS (SHOCKWAVE) - R. Christoffersen, Department of Molecular, Cellular, and Developmental Biology (MCDB), University of California, Santa Barbara Multimedia Genetics Teaching Modules (Text, Images & Videos/Movies). Rrelationship between Chromosome Movements in Meiosis and the Segregation of Alleles in Meiosis "...The purpose of this presentation is to help you understand the movements of chromosomes in meiosis and how Mendelian genes segregate in meiosis..." For more information see Rolf Christoffersen's Home Page or the Department of Molecular, Cellular, and Developmental Biology (MCDB) ESSENTIALS OF GENETICS (SHOCKWAVE) - Authors: William S. King & Michael R. Cummings; Publisher: Prentice Halls Multimedia Genetics Textbook (Text, Images & Videos/Movies). VERY VERY EXTENSIVE. Examples of Essentials of Genetics Chapters include: "...Mitosis & Meiosis; Modification of Mendelian Ratios; Sex Determination and Sex Chromosomes; Quantitative Genetics; DNA Structure & Analysis; Translation of Proteins; Recombinant DNA Technology; Genomics & Proteomics; Genes & Development; Genetics & Evolution; etc..." For more information see Prentice Hall GENETIC POWER CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS GENETIC POWER CALCULATOR - S. Purcell & P. Sham, Psychiatric and Neurodevelopmental Genetics Unit (PNGU), Center for Human Genetic Research (CHGR), Richard B. Simches Research Center, Massachusetts General Hospital & Harvard University VERY VERY VERY...EXTENSIVE. Gemetic Power Calculator "...provides automated power analysis for variance components (VC) quantitative trait locis (QTL) linkage and association tests in sibships, and other common tests..." Gemetic Power Calculators include "...QTL Linkage for Sibships Calculator; QTL Association for Sibships Calculator; TDT for discrete traits Calculator; TDT and parenTDT with ascertainment Calculator; Case - control for discrete traits Calculator; Quantitative TDT Calculator; Case-control for threshold-selected quantitative traits Calculator; Epistasis power Calculator; Probability Function Calculator Calculator; Variance Components - Relative Risk Conversion; etc..." For more information see the Purcell Lab or the Psychiatric and Neurodevelopmental Genetics Unit (PNGU) Some examples from over "13" Gemetic Power Calculators include TDT for Discrete Traits Calculator TDT for Discrete Traits Calculator INPUT Values include: "...High risk allele frequency; Prevalence; Genotype relative risk Aa; Genotype relative risk AA; D-prime; Marker allele frequency; etc..." Quantitative Case-Control Calculator Quantitative Case-Control Calculator INPUT Values include: "...Total QTL variance; QTL increaser allele frequency; Marker M1 allele frequency; Linkage disequilibrium (D-prime); Number of cases; Case lower threshold; Case upper threshold; Control: case ratio; etc..." QTL Association for Sibships Calculator QTL Association for Sibships Calculator INPUT Values include: "...Total QTL variance; Dominance: additive QTL effects; QTL increaser allele frequency; Marker M1 allele frequency; Sample Size; Sibship Size; User-defined type I error rate; etc..." EYE COLOR CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS EYE COLOR CALCULATOR: INHERTING EYE COLOR - Athro, Limited Eye Color Calculator: "...Let's pretend that two genes (with two flavors each) explain the inheritance of human eye color..." For more information see Genetics; Biology or Athro, Limited PEACHFACED LOVEBIRD GENETICS CALCULATORS & APPLETS PEACHFACED LOVEBIRD GENETICS CALCULATOR (JAVA APPLET) - African LoveBird Society Peachfaced Lovebird Genetics Calculator "...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 Genetics (Population) POPULATION GENETICS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS ASSIGNMENT CALCULATOR - J. Brzustowski, Department of Biological Sciences, University of Alberta, Canada VERY VERY VERY...EXTENSIVE. Assignment 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 Department of Biological Sciences POPULATION GENETICS - K. Christensen, Department of Animal and Veterinary Basic Science, Faculty of Life Sciences, University of Copenhagen, Denmark Multimedia Population Genetics Course & Calculators (Text, Images & Videos/Movies). VERY VERY VERY...EXTENSIVE. Population Genetics "...efforts have been made to adjust the notes for students with a biological background, and at the same time supply a minimal set of formulas to describe the relationship between practical observations and genetic theory. In addition to the description of traits with simple Mendelian inheritance, the description of the genetics for traits (diseases) with multifactoriel aetiology has also been emphasized, here the application of correct breeding plans make it possible to significantly lower the frequency of the disease..." Examples of Population Genetics Course Chapters include: "...Introduction, quantitative versus qualitative (Mendelian) genetics; Hardy-Weinberg law for gene frequency stability in large populations; Deviations from Hardy-Weinberg equilibrium; Relationship and inbreeding; Test of simple genetic hypotheses, experimental or field data; Definition of quantitative traits, breeding values and heritability; Estimation of breeding values; Inbreeding, crossing and bred structure; etc..." For more information see Knud Christensen's Home Page or the Department of Basic Animal and Veterinary Sciences or the Faculty of Life Sciences Some examples from over "12" Population Genetics Calculators include Chapter 14: Genetic Calculators, Applets and other Programs Linkage, 3-point Analyses from Test Cross Change in Gene- and Genotype Frequencies, and effect of Population Size Calculation of Corrected Segregation Ratio according to Singles Method POPULATION GENETICS - 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" Population Genetics Calculator include EM Algorithm for ABO Frequencies Calculator EM Algorithm for ABO Frequencies Calculator "...Illustrates the EM algorithm for estimating allele frequencies in the ABO blood system. Users may select from a variety of sample configurations (including random allocation of phenotypes with three different sample sizes) and several different starting guesses (including random frequencies)..." Natural Selection Calculator Natural Selection Calculator "...illustrates how allele frequencies change over time in response to natural selection on diploid genotypes. Users may select from five different fitnesses (0.8, 0.9, 1.0, 1.1, 1.2) for each of the three genotypes. The number of generations is fixed at 100. Results from up to eight different iterations are..." Genetic Drift and Mutation Calculator Genetic Drift and Mutation Calculator "...illustrates the interaction between mutation and genetic drift. Users may select from three different population sizes (25, 100, 250) and several different mutation rates (none, 0.0001, 0.001, 0.01). 32 populations are simulated simultaneously and the results are displayed as a frequency histogram..."

Gene Regulation & Prokaryotes GENE REGULATION CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PROKARYOTES CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PROKARYOTIC DATABASE OF GENE REGULATION AND REGULATORY NETWORKS PRODORIC: PROKARYOTIC DATABASE OF GENE REGULATION - R. Münch, Technical University Carolo-Wilhelmina, Brunswick, Lower Saxony, Germany Multimedia Database & Tools for Visualization & Analysis (Text, Images, Applets). VERY VERY VERY...EXTENSIVE. "...PRODORIC "...is a comprehensive database about molecular networks in prokaryotes with focus on transcriptional regulation..." PRODORIC 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 PRODORIC Tools include Virtual Footprint Virtual Footprint "...is for recognizing single or composite DNA patterns. It was especially designed to analyze transcription factor binding sites in..." PrediSi (Prediction of Signal Peptides) PrediSi is "...a software tool for predicting signal peptide sequences and their cleavage positions in bacterial and eukaryotic proteins..." JVirGel JVirGel allows you to "...Create your own Virtual 2D Gel n two steps..." Glycoscience GLYCOSCIENCES CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS GLYCOSCIENCES TOOLS - A. Bohne-Lang, Molecular Modeling, Central Sectroscopy Department, German Cancer Research Center (DKFZ), Heidelberb, Germany VERY VERY VERY...EXTENSIVE. Multimedia Glycosciences Tools (Text, Images, 3D Modeling, Calculators). For more information see the Andreas Bohne-Lang's Home Page; Central Sectroscopy Department - Molecular Modeling or DKFZ Some Examples of Glycosciences Calculators & Tools includes GlycoFragments Calculator GlycoFragments Calculator "...calculates and displays the main fragments (Band C-, Z- and Y-, A- and X-ions) of oligosaccharides that should occur in MSspectra..." LiGraph LiGraph: "...Convert a sugar graph to ASCII IUPAC sugar nomenclature or as a graph..." Glyvicinity Glyvicinity: "...Analysis of Amino Acids in the Vicinity of Carbohydrate Residues contained in the Protein Data Bank..." Immunology IMMUNOLOGY CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS IMMUNOLOGY LABORATORY CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS MICROBIOLOGY LAB WORK - A. Cann, Microbiology @ Leicester, Department of Biology, School of Biological Sciences, University of Leicester, U.K. Multimedia Microbiology Laboratory Experiments Teaching Modules (Text, Images, Animations & Simulations). VERY VERY EXTENSIVE. Microbiology Laboratory Interactive Experiments include "...Antibody-Antigen Interactions; Mr Campbell's Kidney; Rubella Testing; Gram Stain Procedure; Influenza Virus Haemagglutination; Henrietta Lacks (who dunnit? Find out using PCR!); etc..." For more information see MicrobiologyBytes; Microbiology @ Leicester; Department of Biology or the School of Biological Sciences Examples from over "8" Microbiology Laboratory Interactive Experiments include Antibody-Antigen Interactions In this experiment, you will determine: "...The antibody concentration of a test antiserum; The number of antigenic determinants (antibody binding sites) on an antigen molecule..." Mr Campbell's Kidney: The ELISA (Enzyme Linked ImmunoSorbent Assay) Assay The ELISA (Enzyme Linked ImmunoSorbent Assay) Assay "...Mr Campbell suffers from chronic renal failure. A kidney with a good tissue match to Mr Campbell has just become available for transplantation. However, before the transplant, a blood test reveals that the kidney donor has mononucleosis (a relatively benign increase in the number of monocytes in the blood). Before proceeding with the transplant, Mr Campbell's surgeon has ordered serological tests for Epstein-Barr Virus (Result - negative) and cytomegalovirus (CMV) infection. You will perform the assay for CMV antibodies..." VIRTUAL IMMUNOLOGY (SHOCKWAVE) - Howard Hughes Medical Institute Multimedia Immunology Laboratory Teaching Modules (Text, Images & Animations). VERY EXTENSIVE. The Immunology Lab "...This virtual laboratory will demonstrate how such a test, termed an enzyme-linked immunosorbent assay (ELISA), is carried out and show some of the key experimental problems that may be encountered..." For more information see Howard Hughes Medical Institute OUCHTERLONY ANALYSIS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS OUCHTERLONY ANALYSIS SIMULATOR (JAVA APPLET) - H.R. Gutman & G.A. Gutman, Department of Microbiology and Molecular Genetics, University of California, Irvine (UCI) VERY EXTENSIVE. Ouchterlony Analysis "...In this assay, the antigen and antibody solutions are placed in nearby wells cut into a thin layer of agarose, and allowed to stand for a day or two. They diffuse toward each other, and when they meet at a ratio of equivalence they will form a visible line of precipitate. The pattern in which the lines cross one another can yield considerable information about the antigenic relationships between different antigens..." Ouchterlony Analysis Simulation INPUT Values include: "...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

Metabolic Engineering METABOLIC ENGINEERING CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS METABOLISM CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS METABOLIC ENGINEERING: COMPUTER SIMULATION OF METABOLISM (JAVA APPLETS) - D. Rose, Center for Plant Environmental Stress Physiology, Department of Horticulture and Landscape Architecture, Purdue University VERY VERY VERY...EXTENSIVE. Computer Simulation of Metabolism "...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" Metabolic Engineering Calculators & Applets include Pulse-Chase Labeling Kinetics Simulator Pulse-Chase Labeling Kinetics Simulator With Compartmentation Stable Isotope Pulse-Chase Labeling Kinetics Simulator GS/GOGAT Cycle Simulator Radiolabeling Kinetics Simulator Radiolabeling Kinetics Simulator Assuming Fixed Rates of Modeling Molecular Biology & Bioinformatics MOLECULAR BIOLOGY CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS MOLECULAR BIOLOGY PROTOCOLS - CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS 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. Available in English German/Deutsch, Russian & Ukrainian. Molecular Biology Calculators Subject Categories include: "...Salt Solution Calculators; Laboratory Buffer Calculators; Single Component Solution Calculators; Compound Solution Calculators; Antibiotic Solution Calculators; etc..." For more information see Practical Molecular Biology Some examples from over "100" Molecular Biology Protocols Calculators Antibiotic Solution Calculators Antibiotic Solution Calculators include: "...Working Concentrations and Stock Solutions Calculator; Preparation of Stock Solutions for Ampicillin Calculator; Preparation of Stock Solutions for Carbenicillin Calculator; Preparation of Stock Solutions for Chloramphenicol Calculator; etc.." Single Component Solutions Calculators Single Component Solutions Calculators include: "...Organic Substances Calculators include: ATP Calculator; Betaine Calculator; EDTA Calculator; EtBr Calculator; Gelatin Calculator; HEPES Calculator; PEGV; Sucrose Calculator; etc. Acids and Alkalis Calculators; Detergents Calculator; Organic Solvents Calculators; etc..." Compound Solutions Calculators Compound Solutions Calculators include: "...Electrophoresis Buffer Calculator; Loading Buffer Calculator; Bacteriophage Lambda Buffer Calculator; Denaturation Buffer Calculator; Neutraliszation Buffer Calculator; Plasmid Solution Calculator; Oligonucleotide Gel Staining Mix Calculator; etc..." Spectrophotometric Measurement of Nucleic Acids Concentrations Calculator Spectrophotometric Measurement of Nucleic Acids Concentrations Calculator "...calculates the concentration of nucleic acids according to their optical density: DNA, RNA, Oligonucleotides,..." Estimation of Time for Bacteria Growth Calculator Estimation of Time for Bacteria Growth Calculator: "...This is important for the preparation of chemical- or electro-competent cells and protein expression. The program may be used also for other organisms in the logarithmic stage of growth..." PCR Optimization Calculator PCR Optimization Calculator "...helps to evaluate the quantity of primers and nucleotides for optimal PCR reaction and the necessary number of cycles..." Radioactivity to Biological Amount of dNTPs Calculator Radioactivity to Biological Amount of dNTPs Calculator calculates the "...weight of particular amount of radioactive dNTPs..." MOLECULAR BIOLOGY CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS BIOINFORMATICS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS BIOINFO BANK - BioInfo Bank, Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Japan VERY VERY VERY...EXTENSIVE. For more information see the Department of Bioscience and Bioinformatics or the Kyushu Institute of Technology (KIT) Some examples of Bioinformatics Databases, Calculators & Tools include 3DinSight 3DinSight "...is an integrated database and search tool for structure, property and function of biomolecules. 3DinSight is developed to help researchers to get insight into the relationship among the structure, property and function of biomolecules..." ProTherm ProTherm "...is a collection of numerical data of thermodynamic parameters such as Gibbs free energy change, enthalpy change, heat capacity change, transition temperature etc. for wild type and mutant proteins, that are important for understanding the structure and stability of proteins. It also contains information about secondary structure and accessibility of wild type residues,..." Protein-Nucleic Acid Complex Protein-Nucleic Acid Complex "...is a database containing structural data of protein-nucleic acid complex. These data are classified according to recognition motif of proteins and DNA forms involved in the complex. The search interface enables users to search the database by keywords, recognition motif, DNA form, etc., and the..." BIOINFORMATICS TOOLS AND RESOURCES FOR BIOMEDICAL SCIENTISTS AND STUDENTS - Chang Bioscience, Inc. VERY VERY VERY...EXTENSIVE. For more information see Chang Bioscience, Inc. Some examples from over "20" Bioinformatics Calculators include Log-odds Ratio Calculator Log-odds Ratio Calculator INPUT Values include "...Risk Ratio; Odds Ratio..." Genetic Screen Number of Progeny Calculator Genetic Screen Number of Progeny Calculator INPUT Values include "...Expected Recombination Rate Percentage; Confidence Percentage..." Tetrad Calculator Tetrad Calculator INPUT Values include "...Choose a Cross Type; Edit Gene Names; Number of Genes..." Hemocytometer Cell Count Calculator Hemocytometer Cell Count Calculator INPUT Values include "...Cell Dilution; Cell/Dye Ratio; Cell Count; Viable Cell Concentration; etc..." Probe Fluorescent Labeling Calculator Probe Fluorescent Labeling Calculator INPUT Values include "...Extinction Coefficient; Absorbance; Total Volume; etc..." 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 Some examples of Bioinformatics Databases, Calculators & Tools include Protein Colourer Protein Colourer is "...a tool for colouring your amino acid sequences. The default settings will colour the sequence by the hydrophobicity of the amino acids. You can set the colouring scheme by changing the lists associated with each colour..." Protein Functional Analysis Protein Functional Analysis is "...used in the determination of protein function using various methods and databases..." Expression Profiler Expression Profiler "...is an open, extensible web-based collaborative platform for microarray gene expression, sequence and PPI data analysis, exposing distinct chainable components for clustering, pattern discovery, statistics (thru R), machine-learning algorithms and visualization..." EXPASY PROTEMOICS TOOLS - ExPASy Proteomics Server, Swiss Institute of Bioinformatics, Geneva, Switzerland VERY VERY VERY...EXTENSIVE. For more information see ExPASy Proteomics Server Some examples from over "100" ExPASy Proteomics Databases, Calculators & Tools include Aldente Aldente "...is a tool to identify proteins from peptide mass fingerprinting data. This new, fast and powerful tool takes advantage of the Hough transform for spectra recalibration and outlier exclusion..." GlycoMod GlycoMod "...is a tool that can predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses. The program can be used for free or derivatized oligosaccharides and for glycopeptides..." FindPept FindPept "...can identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage..." ONLINE ANALYSIS TOOLS - A.M. Kropinski, Department of Microbiology & Immunology, Queen's University, Kingston, Ontario, Canada VERY VERY EXTENSIVE. Online Analysis Tools are "...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 the Department of Microbiology & Immunology

Molecular Mass, Molar Mass, Exact Mass, Elemental Composition, Isotope Ratios, etc. MOLECULAR MASS, EXACT MASS, ELEMENTAL ANALYSIS CALCULATORS & APPLETS CHEMCALC (JAVA APPLET) - ChemExper sprl, Belgium VERY EXTENSIVE. CHEMCALC Calculator "...calculates the Molecular Formula, Molecular Mass, Exact Mass, Elemental Analysis and Plots the Isotopic Distribution Graph... For more information see ChemExper MOLAR MASS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS MOLARITY CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS MOLARITY CALCULATOR: CREATE AND DILUTE MOLAR SOLUTIONS - H. Motulsky, GraphPad Software, Inc. VERY EXTENSIVE. Molarity Calculators include: "...Mass from Volume & Concentration Calculator; Volume from Mass & Concentration Calculator; Molarity from Mass & Volume Calculator; Dilute a Stock Solution Calculator..." For more information see Chemical and Radiochemical Calculators; GraphPad QuickCalcs or GraphPad Software MOLAR MASS AND PERCENT BY MASS CALCULATOR - D. Wookcock, Department of Chemistry, Okanagan University College, B.C., Canada VERY EXTENSIVE. Molar Mass Calculator and Percent by Mass Calculator "...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 Dave Woodcock's Home Page or the Department of Chemistry MOLAR MASS CALCULATOR - First Year Chemistry, School of Chemistry, University of Sydney, Sydney, Australia Molar Mass Calculator "...Enter a chemical formula of a compound (e.g. H2O) to calculate molar mass and elemental composition..." For more information see Chemical Calculators; First Year Chemistry or the School of Chemistry MOLAR MASS CALCULATOR - V. Vanovschi Molar Mass Calculator "...Enter a chemical formula of a compound (e.g. H2SO4) to calculate molar mass and elemental composition..." For more information see Vitalii Vanovschi's Home Page or MOLECULAR MASS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS WELCOME TO THE FORMULA TO MASS TO FORMULA APPLET PAGE - G. Cottenceau, Department of Chemistry, Imperial College of Science, Medicine and Technology, U.K. VERY EXTENSIVE. For more information see Examples of the Application of Java to Chemistry CHEMIE.DE MOLECULAR MASS CALCULATOR - Chemie.DE Information Service GmbH, a Life Science Network Division VERY EXTENSIVE. Molecular Mass Calculator lets "...you calculate the mass of a molecule..." For more information see Chemie DE CALCULATE ELEMENTAL COMPOSITION FROM A GIVEN MOLECULAR MASS ELEMENTAL COMPOSITION CALCULATOR - J.A. McCloskey, P.F. Crain, & J. Rozenski, Huntsman Cancer Institute, University of Utah Elemental Composition Calculator "...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 VERY EXTENSIVE. Molecular Mass Calculator "...Calculates molecular masses and isotope ratios from elemental compositions..." For more information see the Nucleic Acids Masspec Toolbox or the Huntsman Cancer Institute Molecular & Atomic Weight MOLECULAR WEIGHT CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS ATOMIC WEIGHT CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS MOLECULAR FORMULA FROM A HRMS WEIGHT CALCULATORS & APPLETS FIND MOLECULAR FORMULA FROM A HRMS WEIGHT (JAVA APPLET) - J.M. Goodman, Department of Chemistry, Cambridge University VERY VERY EXTENSIVE. Molecular Formula from a HRMS Weight Calculator "...can be interrupted part way through, and the elements which have been fully investigated will be listed. The elements are searched in order of probable occurence, beginning the C, H, O then N. If chemical check is highlighted, then the search will exclude molecules which should not exist as single molecules..." For more information see Magnus: Chemical Calculations in Java; Tools; Goodman Group; Jonathan M. Goodman's Home Page or the Department of Chemistry MOLECULAR WEIGHT CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS MOLECULAR WEIGHT CALCULATION (JAVA APPLET) - J.M. Goodman, Department of Chemistry, Cambridge University VERY EXTENSIVE. Molecular Weight Calculator INPUT Values include: "...Input Molecular Formula..." Molecular Weight Calculator OUTPUT Values include: "...HRMS Weight; Molecular Weight; Element Percentage; Standardised Molecular Formula; Molecular Ion Isotope Pattern..." For more information see Magnus: Chemical Calculations in Java; Tools; Goodman Group; Jonathan M. Goodman's Home Page or the Department of Chemistry MOLECULAR WEIGHT CALCULATOR (JAVA APPLET) - ChemicalLogic Molecular Weight Calculator INPUT Values include: "...Input Molecular Formula..." Molecular Weight Calculator ouput values include: "...Molecular Weight..." For more information see ChemicalLogic Corporation MOLECULAR WEIGHT CALCULATION - Institut für Chemie (Institute of Chemistry), Freie Universität Berlin, Germany VERY EXTENSIVE. Molecular Weight Calculator INPUT Values include: "...Input Molecular Formula..." Molecular Weight Calculator OUTPUT Values include: "...Molecular Weight; Physical Molecular Weight; Elemental Analysis; Double Bond Equivalents..." For more information see the Institute of Chemistry (English Version) or Institut für Chemie (Deutsch Version) RNA MOLECULAR WEIGHT CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS DNA MOLECULAR WEIGHT CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PROTEIN MOLECULAR WEIGHT CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS DNA, RNA, PROTEIN, CHEMICAL MOLECULAR WEIGHT CALCULATOR - Chang Bioscience, Inc. VERY VERY EXTENSIVE. DNA, RNA, Protein,Chemical Molecular Weight Calculator "...For DNA/RNA molecular weight, users have the option to input sequences or sequence length. Degenerate codes can be accepted. Blanks and numbers will be automatically ignored. For modified DNA/RNA or for primer/oligo calculations, please use the Oligo Calculator. For protein/peptide molecular weight, users have the option to input sequences or sequence length. If sequences are inputed, they must in the single-letter codes. Blanks and numbers will be automatically ignored..." Molecular Weight Calculators include "...Protein Molecular Weight Calculator; Single-Stranded DNA Molecular Weight Calculator; Double-Stranded DNA Molecular Weight Calculator; RNA Molecular Weight Calculator; etc..." For more information see Chang Bioscience, Inc. PROTEIN MOLECULAR WEIGHT CALCULATOR - S. Venkataraman, Michigan State University VERY EXTENSIVE. Protein Molecular Weight Calculator INPUT Values include: "...Molar Weight of the First Marker; Molar Weight of the Second Marker; Distance of First Marker; Distance of Second Marker; Distance of Unknown; etc..." For more information see JavaScript or Sridhar Venkataraman's Home Page

Multiple Alignments MULTIPLE ALIGNMENTS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS 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. Colour Interactive Editor for Multiple Alignments (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 Neural Networks & Artifical Life ARTIFICIAL LIFE CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS CELLULAR AUTOMATA CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS NEURAL NETWORKS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS ARTIFICIAL LIFE - CELLULAR AUTOMATA (JAVA APPLETS) - I. Yoshiaki, Japan VERY VERY VERY EXTENSIVE. For more information see Ishihama Yoshiaki's Home Page Some examples from over "120" Artificial Life Applets, Neural Networks Applets & Cellular Automata Applets include Boid Applet Fishes2 Applet Ants (Wireframe) Applet Tarantula Applet MicroOrganism: Bacillus Applet Langtons Loop Applet ARTIFICIAL LIFE - D. Griffeath, Mathematics Department, Cornell University VERY VERY EXTENSIVE. For more information see David Griffeath's Home Page Examples of Artifical Applets & Cellular Automata Applets include Mirek's Java Cellebration (MJCell) Mirek's Java Cellebration (MJCell) "...allows playing 300+ Cellular Automata rules and 1400+ patterns. It can play rules from 13 CA rules families: Generations, Life, Vote, Weighted Life, Rule tables, Cyclic CA, 1D totalistic, 1D binary, Neumann binary, General binary, Margolus neighborhood, Larger than Life, and some of the User DLLs. It allows also..." Greenberg-Hastings Models Greenberg-Hastings (GH) Model "...is perhaps the simplest CA prototype for an excitable medium..." Life Without Death: Some Elementary Interactions Life Without Death: Some Elementary Interactions "...We demonstrate six of the basic ladder interactions used to show that the Life Without Death rule is capable of emulating Boolean circuits..." NEURAL NET CONCEPTS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS NEURAL NET CONCEPTS (JAVA APPLET) - Computation and Neural Networks Laboratory. Department of Electrical & Computer Engineering, College of Engineering, Wayne State University VERY VERY EXTENSIVE. For more information see Computation and Neural Networks Laboratory Examples from over "20" Neural Net Applets include Extreme Point Machine (EPM): 2-D 2-Class VersionL 2D Time Dynamical System

Nucleic Acids - Nucleotide Mass NUCLEIC ACID CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS NUCLEOTIDE MASS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS NUCLEIC ACIDS MASSPEC TOOLBOX - J.A. McCloskey, P.F. Crain, & J. Rozenski, Huntsman Cancer Institute, University of Utah VERY VERY EXTENSIVE. For more information see the Huntsman Cancer Institute Some examples of Nucleic Acids Massspec Calculators include Mongo Oligo Mass Calculator Oligonucleotide Mass Calculator "...includes mass calculation of oligonucleotides, CID fragments, endo- and exonuclease digestion. It contains extra output options and utilities for handling the input sequence and user residue assignment..." Oligo Composition Calculator Oligo Composition Calculator "...Finds nucleotide compositions from a given mass. User defined residues can be included..." Oligonucleotide OLIGONUCLEOTIDE CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS MONGO OLIGO MASS CALCULATORS & APPLETS MONGO OLIGO MASS CALCULATOR - J.A. McCloskey, P.F. Crain, & J. Rozenski, Huntsman Cancer Institute, University of Utah VERY VERY EXTENSIVE. Oligonucleotide Mass Calculator "...includes mass calculation of oligonucleotides, CID fragments, endo- and exonuclease digestion. It contains extra output options and utilities for handling the input sequence and user residue assignment..." For more information see the Nucleic Acids Masspec Toolbox or the Huntsman Cancer Institute OLIGO CALCULATOR - E. Buehler, Department of Molecular Gnentics & Biochemistry, University of Pittsburgh Oligonucleotide Calculator INPUT Values include: "...Enter Oligonucleotide Sequence..." For more information see Department of Molecular Gnentics & Biochemistry OLIGONUCLEOTIDE MW AND EXTINCTION COEFFICIENT CALCULATORS & APPLETS OLIGONUCLEOTIDE MW AND EXTINCTION COEFFICIENT CALCUCLATOR - Ambion, Inc VERY VERY EXTENSIVE. Oligonucleotide MW and Extinction Coefficient Calculator "...can be used to determine the molecular weight and extinction coefficient of a chemically synthesized DNA or RNA oligonucleotide..." For more information see Ambion Technical Resources or Ambion OLIGONUCLEOTIDE PROPERTIES CALCULATORS & APPLETS OLIGONUCLEOTIDE PROPERTIES CALCULATOR - Q. Cao, Northwestern University Medical School, Northwestern University VERY VERY EXTENSIVE. For more information see Basic Sciences Peptide Mass PEPTIDE CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PEPTIDE CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS ACCURATE MASS & PEPTIDE MODIFICATION ACCURATE MASS & PEPTIDE MODIFICATION - A. Bohne-Lang, Molecular Modeling, Central Sectroscopy Department, German Cancer Research Center (DKFZ), Heidelberb, Germany VERY VERY EXTENSIVE. Peptide Accurate Mass Calculator & Peptide Modification Calculator "...Two levels of support are offered: Level 1 deliveres a display of the input deltamass value relative to the distribution of peptide deltamass values extracted from the nrdb database. In case the deltamass value is indicative of a glycopeptide, level 2 can be used to generate a list of proposed N-glycan structures when the sequence of the stem protein is known..." For more information see the Andreas Bohne-Lang's Home Page or the Central Sectroscopy Department - Molecular Modeling PEPTIDE MASS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PEPTIDE MASS CACLULATOR - R.C. Beavis & hosted by Peptide Protein Research Ltd. Peptide Mass Calculator: "...Use this handy calculator to work out the mass of your amino acid sequence. It handles n-terminal modifications, oxidized cysteines and phosphorylated amino acids..." For more information see Peptide Synthesis PEPTIDE MASS CACLULATOR - J. Rozenski, Bio Analytical Mass Spectrometry Facility, Rega Institute for Medical Research, Belgium VERY EXTENSIVE. Peptide Mass Calculator INPUT Values include: "...Sequence; N-terminal Group; C-Terminal Group; User Defined; Calculate Molecular Mass, [M+H]+, ES Series Positive Mode or ES Series Negative Mode; using Average Masses or Monoisotopic Masses..." For more information see Mass Calculators or the Bio Analytical Mass Spectrometry Facility PEPTIDE MASS - ExPASy Proteomics Server, Swiss Institute of Bioinformatics, Geneva, Switzerland VERY VERY EXTENSIVE. Peptide Mass Calculator "...cleaves a protein sequence from the UniProt Knowledgebase (Swiss-Prot and TrEMBL) or a user-entered protein sequence with a chosen enzyme, and computes the masses of the generated peptides. The tool also returns theoretical isoelectric point and mass values for the protein of interest..." For more information see ExPASy Proteomics Tools or ExPASy Proteomics Server

Proteins PROTEIN CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PROWL - PROWL, Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University VERY VERY EXTENSIVE. Examples of Prowl Tools & Calculators include: ProFound "...a tool for searching a protein sequence collections with peptide mass maps..." ProteinInfo "...a collection of tools for retrieval and analysis of protein sequences..." PeptideMap "...PeptideMap is a tool for finding modifications on polypeptide sequences..." PepFrag "...a tool for identifying proteins from a collection of sequences that matches a single tandem mass spectrum..." X! Tandem "...a tool for identifying proteins from a collection of peptide sequences that matches tandem mass spectra..." X! Hunter; GPMDB; etc..." For more information see PROWL EXPASY PROTEMOICS TOOLS - ExPASy Proteomics Server, Swiss Institute of Bioinformatics, Geneva, Switzerland VERY VERY VERY...EXTENSIVE. For more information see ExPASy Proteomics Server Some examples from over "100" ExPASy Proteomics Databases, Calculators & Tools include Aldente Aldente "...is a tool to identify proteins from peptide mass fingerprinting data. This new, fast and powerful tool takes advantage of the Hough transform for spectra recalibration and outlier exclusion..." GlycoMod GlycoMod "...is a tool that can predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses. The program can be used for free or derivatized oligosaccharides and for glycopeptides..." FindPept FindPept "...can identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage..." BRADFORD TEST BY REGRESSION ANALYSIS BRADFORD TEST BY REGRESSION ANALYSIS - CALCULATOR - S. Venkataraman, Michigan State University VERY EXTENSIVE. Bradford test by Regression Analysis Calculator "...evaluates protein concentrations based on OD595..." For more information see JavaScript or Sridhar Venkataraman's Home Page PROTEIN MOLECULAR WEIGHT CALCULATORS & APPLETS DNA, RNA, PROTEIN, CHEMICAL MOLECULAR WEIGHT CALCULATOR - Chang Bioscience, Inc. VERY VERY EXTENSIVE. DNA, RNA, Protein,Chemical Molecular Weight Calculator "...For DNA/RNA molecular weight, users have the option to input sequences or sequence length. Degenerate codes can be accepted. Blanks and numbers will be automatically ignored. For modified DNA/RNA or for primer/oligo calculations, please use the Oligo Calculator. For protein/peptide molecular weight, users have the option to input sequences or sequence length. If sequences are inputed, they must in the single-letter codes. Blanks and numbers will be automatically ignored..." Molecular Weight Calculators include "...Protein Molecular Weight Calculator; Single-Stranded DNA Molecular Weight Calculator; Double-Stranded DNA Molecular Weight Calculator; RNA Molecular Weight Calculator; etc..." For more information see Chang Bioscience, Inc. PROTEIN MOLECULAR WEIGHT CALCULATOR - S. Venkataraman, Michigan State University VERY EXTENSIVE. Protein Molecular Weight Calculator INPUT Values include: "...Molar Weight of the First Marker; Molar Weight of the Second Marker; Distance of First Marker; Distance of Second Marker; Distance of Unknown; etc..." For more information see JavaScript or Sridhar Venkataraman's Home Page Protein - Calcium Binding Proteins PER RESIDUE SOLVENT ACCESSIBLE SURFACE CALCULATORS & APPLETS PER RESIDUE SOLVENT ACCESSIBLE SURFACE CALCULATOR - Developed by M. Nelson, The EF-Hand Calcium Binding Proteins Data Library; Walter Chazin's Laboratory, Vanderbilt University VERY EXTENSIVE. Per Residue Solvent Accessible Surface Calculator will "...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 VERY VERY EXTENSIVE. Homolog Finder for EF-Hand Calcium-Binding Proteins Calculator "...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 FOLDING CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PROTEIN & MACROMOLECULES MOVEMENTS/MOTIONS - MOVIES, SIMULATIONS MOLECULAR MOVEMENTS DATABASE - N. Echols, Bioinformatics Web Server, Department of Molecular Biophysics and Biochemistry, Yale University Multimedia Molecular Movements Database (Text, Images & Videos/Movies). VERY VERY VERY...EXTENSIVE. Molecular Movements 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 Molecular Movements Alternative URL #1; Molecular Movements Alternative URL #2 or the Bioinformatics Web Server [GdmCl] AND [UREA] CALCULATORS & APPLETS [GdmCl] AND [UREA] CALCULATOR - T. Sosnick, Sosnick Group, Folding & Design, Department of Biochemistry & Molecular Biology, University of Chicago VERY EXTENSIVE. [GdmCl] and [Urea] Calculator INPUT Values include "...Buffer Refractive Index; Denaturant Refractive Index..." For more information see Sosnick Group or the Department of Biochemistry & Molecular Biology [GuHCl] AND [UREA] CALCULATORS & APPLETS [GuHCl] AND [UREA] CALCULATOR - D. Baker, The Baker Laboratory (Protein Folding), Department of Biochemistry, University of Washington [GdmCl] and [Urea] Calculator INPUT Values include "...Buffer Refractive Index; Sample Refractive Index..." For more information see The Baker Laboratory or the