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, June 18, 2013 Sydney, Australia: Wednesday, June 19, 2013 File Download Time Calculator Author, E-Mail, Privacy Policy & Disclaimer Currently the Calculators On-Line Center contains over "24,475" Calculators & Spreadsheets, over "4,200" 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 Immunology ~ Metabolic Engineering Molecular Biology & Bioinformatics Molecular Mass, Molar Mass, Exact Mass, Molarity, Elemental Composition, Isotope Ratios, etc. Molecular Weight Neural Networks & Artificial Life 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 - Analytical Ultracentrifugation Facility (AUF), Biotechnology-Bioservices Center (BBC), University of Connecticut VERY VERY VERY...EXTENSIVE. Analytical Ultracentrifugation "...software for the manipulation and analysis of ultracentrifugation data..." For more information see the Analytical Ultracentrifugation Facility (AUF) or the Biotechnology-Bioservices Center (BBC) 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; Jeffery L. Ram's Faculty 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 Botany FOR BOTANY RELATED CENTERS WITH CALCULATORS, COURSES, DATABASES, ETC. SEE THE AGRICULTURE CENTER OR THE GARDENING & BOTANY CENTER 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 & Statistics, 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 & Statistics 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 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 CALCULATOR - 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 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 Buffers for pH Control 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.J. Bezanilla (Emeritus), Brain Research Institute (Brain Research Foundation), Division of Biological Sciences, University of Chicago and the Department of Physiology, David Geffen School of Medicine, UCLA Multimedia Electrophysiology Textbook, Lessons, 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 the Brain Research Foundation; Division of Biological Sciences, University of Chicago; Department of Physiology, David Geffen School of Medicine, UCLA 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 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. 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 Cognition COGNITION CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS COGNITIVE CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS 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, Max-Planck-Institut fur Molekulare Genetik (Max Planck Institute for Molecular Genetics), Berlin, Germany VERY VERY VERY...EXTENSIVE. Zbio.net "...is created and supported by the Aleksey Soldatov and Tanja Borodina at Max-Planck-Institut fur Molekulare Genetik..." Available in English, German/Deutsch, Russian & Ukrainian. Examples of "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 Zibo.net; Zibo.net Protocols Alternate Site or the Max-Planck-Institut fur Molekulare Genetik (Max Planck Institute for Molecular Genetics) Examples from over "100" Molecular Biology Protocols Calculators Antibiotic Solution Calculators Examples of "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 Examples of "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 Examples of "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,..." Time Estimation for Bacteria Growth Calculator Time Estimation 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..."

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 Electrophoresis ELECTROPHORESIS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS 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 Lessons (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 the Department of Chemistry 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 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 TRIS-GLYCINE SDS-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 ESSENTIALS OF GENETICS (FLASH) - 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 Genetics (Population) POPULATION GENETICS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS POPULATION GENETICS - K. Christensen, Department of Animal and Veterinary Basic Science, Faculty of Science, 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; Department of Basic Animal and Veterinary Sciences or the Faculty of Science 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..." 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..." 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 (Text, Images, Animations & Simulations). VERY VERY EXTENSIVE. Examples of "Microbiology Laboratory 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; Alan Cann's Home Page; Department of Biology or the School of Biological Sciences Examples from over "8" "Microbiology Laboratory Experiments" include Antibody-Antigen Interactions 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 (FLASH) - Howard Hughes Medical Institute Multimedia Immunology Laboratory Lessons (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

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, Max-Planck-Institut fur Molekulare Genetik (Max Planck Institute for Molecular Genetics), Berlin, Germany VERY VERY VERY...EXTENSIVE. Zbio.net "...is created and supported by the Aleksey Soldatov and Tanja Borodina at Max-Planck-Institut fur Molekulare Genetik..." Available in English, German/Deutsch, Russian & Ukrainian. Examples of "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 Zibo.net; Zibo.net Protocols Alternate Site or the Max-Planck-Institut fur Molekulare Genetik (Max Planck Institute for Molecular Genetics) Examples from over "100" Molecular Biology Protocols Calculators Antibiotic Solution Calculators Examples of "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 Examples of "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 Examples of "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,..." Time Estimation for Bacteria Growth Calculator Time Estimation 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 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 Institute (EBI), European Molecular Biology Laboratory (EMBL), U.K. VERY VERY VERY...EXTENSIVE. Examples of EBI Subject Categories with Datatbases, Calculators, etc. include "...DNA & RNA - Genes, Genomes & Variation; Gene Expression - RNA, Protein & Metabolite Expression; Proteins - Sequences, Families & Motifs; Structures - Molecular & Cellular Structures; Systems - Reactions, Interactions & Pathways; Chemical Biology - Chemogenomics & Metabolomics; Ontologies; etc..." For more information see the European Bionformatics Institute EXPASY: SIB BIOINFORMATICS RESOURCES - ExPASy: SIB Bioinformatics Resource Portal, Swiss Institute of Bioinformatics, Geneva, Switzerland VERY VERY VERY...EXTENSIVE. For more information see ExPASy: SIB Bioinformatics Resource Portal 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, Professor Emeritus, UBC (Okanagan), 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 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 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 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 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.

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 (Emeritus), Mathematics Department, Cornell University VERY VERY EXTENSIVE. For more information see David Griffeath's Home Page or David Griffeath's Faculty 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

Oligonucleotide OLIGONUCLEOTIDE CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS 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 MASS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PEPTIDE MASS CALCULATOR - 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 CALCULATOR - 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: SIB Bioinformatics Resource Portal, 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 SIB Bioinformatics Resources or ExPASy: SIB Bioinformatics Resource Portal

Proteins PROTEIN CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PROWL - Brian T. Chait, 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 or the Laboratory of Mass Spectrometry and Gaseous Ion Chemistry EXPASY: SIB BIOINFORMATICS RESOURCES - ExPASy: SIB Bioinformatics Resource Portal, Swiss Institute of Bioinformatics, Geneva, Switzerland VERY VERY VERY...EXTENSIVE. For more information see Resources or ExPASy: SIB Bioinformatics Resource Portal 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 - 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 - PROTEIN MOTIONS - Mark Gerstein's Lab, 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 Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis or Mark Gerstein's Lab [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 Department of Biochemistry Protein Identification PROTEIN IDENTIFICATION CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS EXPASY: SIB BIOINFORMATICS RESOURCES - ExPASy: SIB Bioinformatics Resource Portal, Swiss Institute of Bioinformatics, Geneva, Switzerland VERY VERY VERY...EXTENSIVE. For more information see Resources or ExPASy: SIB Bioinformatics Resource Portal PEPFRAG CALCULATORS & APPLETS PEPFRAG CALCULATOR (JAVA) - Brian T. Chait, Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University PepFrag "...is a tool for identifying proteins from a collection of sequences that matches a single tandem mass spectrum..." For more information see PROWL or the Laboratory of Mass Spectrometry and Gaseous Ion Chemistry PROTEIN PROSPECTOR CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PROTEIN PROSPECTOR - A.L. Burlingame, Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, School of Pharmacy, UCSF VERY VERY VERY...EXTENSIVE. For more information see the Department of Pharmaceutical Chemistry Protein Translation PROTEIN TRANSCRIPTION AND TRANSLATION CALCULATORS & APPLETS TRANSCRIPTION AND TRANSLATION TOOL - Attotron Biosensor Corporation VERY EXTENSIVE. Transcription and Translation Tool "...Converts DNA to RNA to protein..." For more information see Sequence Analysis Software; QuizMaker Suite or Attotron Biosensor Corporation

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