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MARTINDALE'S
CALCULATORS ON-LINE CENTER SCIENCE A-Z BIOSCIENCE & BIOTECHNOLOGY |
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:
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,..." WINDCDT; WINNONLIN; WINMATCH; WINREEDIT; HETEROANALYSIS - National Analytical Ultracentrifugation Facility (NAUF) VERY VERY VERY...EXTENSIVE. "...software for the manipulation and analysis of ultracentrifugation data..." For more information see the National Analytical Ultracentrifugation Facility (NAUF) Axon Potential
"...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
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:
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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
PHYLLOTAXIS APPLETS - P. Atela-Cortés & C. Golé, Department of Mathematics, Smith College VERY VERY EXTENSIVE. "...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
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..." |
Biological Buffer Calculator includes
BUFFER CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
"...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:
Pyridine; Bis-tris; ADA; PIPES; ACES; Phosphate; Tricine; etc..." Ionic Strength; Control Ionic Strength; Prepare Buffer at Tempterature; Use Buffer at Temperature. CITRIC ACID 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
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..." |
Cell Biology
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
Examples of "Electrophysiology and The Molecular Basis of Excitability" includes:
"...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..."
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..."
Equivalent Circuit of The Axon Simulation
Sodium Channel Simulation Sodium Channel Simulation
Nerve Simulation Nerve Simulation
Cell Electrophysiology Simulation Environment (CESE)
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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..." s 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; and 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
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
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
Brown & Hulme Model
Positional Distinctiveness (Nairne et al., 1997) Positional Distinctiveness Model
Johnson's Distinctiveness Model (Johnson, 1991) Johnson's Distinctiveness Model
SIMPLE: Absolute Identification (Neath, Brown, McCormack, Chater, & Freeman, 2006) Scale Invariant Memory and Perceptual Learning (SIMPLE) Model
Recognition Memory Simulation Recognition Memory Simulation includes
Heuristic Calculator
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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. Also available in 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
Antibiotic Solution Calculators include:
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:
Detergents Calculator; Organic Solvents Calculators; etc..." Compound Solutions Calculators Compound Solutions Calculators include:
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 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 CALCULATOR - S. Venkataraman, Michigan State University DNA Concentration Calculator inputs 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 |
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 computational procedure that is used to identify sequence tagged sites (STSs), within DNA sequences. e-PCR looks for potential STSs in DNA sequences..." 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. 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. "...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 "...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 inputs 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 Calculator "...estimates amounts of DNA to be used for a blunt end ligation..." For more information see JavaScript or Sridhar Venkataraman's Home Page |
Capilary Electrophoresis Calculator input values include:
Injection Plug Length; Plug Percentage Length to Window; Capillary Volumes Replaced; Seconds to replace 1 volume; Injection Pressure-seconds; Relative Viscosity..." 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
"...These animations support the teaching of concepts in chemistry in freshman through graduate level courses..." Subject Categories of Chemistry Laboratory Video Demonstrations & Experiments include:
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..."
ELECTROPHORESIS SIMULATION OF DNA - CALCULATORS & APPLETS
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
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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 "...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
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. |
GENETIC CODE EVOLUTION CALCULATORS & APPLETS CAI CALCULATOR - S.J. Freeland, Freeland Bioinformatics Laboratory, Department of Biological Sciences, University of Maryland VERY VERY EXTENSIVE. Codon Adaptation Index Calculator (CAI Calculator)
"...CAI assumes that the reference set of genes are under selection therefore can be used to estimate the fitness of each codon during the selection. However, this assumption does not always hold. For instance, the translational selection may not exist in some genomes especially those GC-biased genomes. If this assumption does not hold, the CAI values can be hard to interpret..."
Synthetic Gene Designer
GENETIC COURSES WITH CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
"...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 Introduction to Genetics; 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:
Sex Determination and Sex Chromosomes; Quantitative Genetics; DNA Structure & Analysis; Translation of Proteins; Recombinant DNA Technology; Genomics & Proteomics; Genes & Development; Genetics & Evolution; etc..." GENETIC POWER CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
Gemetic Power 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..."
TDT for Discrete Traits Calculator INPUT Values include:
Genotype relative risk AA; D-prime; Marker allele frequency; etc..." Quantitative Case-Control Calculator Quantitative Case-Control Calculator INPUT Values include:
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:
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:
PEACHFACED LOVEBIRD GENETICS CALCULATORS & APPLETS
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 |
Assignment Calculator
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
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..."
EM Algorithm for ABO Frequencies Calculator
Natural Selection Calculator Natural Selection Calculator
Genetic Drift and Mutation Calculator Genetic Drift and Mutation Calculator
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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:
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..." |
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
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
Mr Campbell's Kidney; Rubella Testing; Gram Stain Procedure; Influenza Virus Haemagglutination; Henrietta Lacks (who dunnit? Find out using PCR!); etc..."
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
The Immunology Lab
OUCHTERLONY ANALYSIS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
Ouchterlony Analysis
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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. "...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
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MOLECULAR BIOLOGY PROTOCOLS - CALCULATORS - A. Soldatov, Institute of Gene Biology, Russian ELectronic Academic & Research Network Association (RAS), Moscow, Russia & the Max-Planck-Institut fur Molekulare Genetik, Berlin, Germany VERY VERY VERY...EXTENSIVE. Also available in German/Deutsch, Russian & Ukrainian. 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
Antibiotic Solution Calculators include:
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:
Detergents Calculator; Organic Solvents Calculators; etc..." Compound Solutions Calculators Compound Solutions Calculators include:
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..." |
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)
3DinSight: "...Search tool for structure, property and function of biomolecules..." ProTherm ProTherm: "...Search data of thermodynamic parameters such as Gibbs free energy change, enthalpy change, heat capacity change, transition temperature etc..." Protein-Nucleic Acid Complex Protein-Nucleic Acid Complex: "...Search for data containing structural data of protein-nucleic acid complex..."
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..."
Protein Colourer is "...a tool for colouring your amino acid sequences..." 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,..."
Aldente is "...a tool to identify proteins from peptide mass fingerprinting data..." GlycoMod GlycoMod is "...a tool that can predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses..." FindPept FindPept "...can identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications..." 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 |
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 CALCULATOR: CREATE AND DILUTE MOLAR SOLUTIONS - H. Motulsky, GraphPad Software, Inc. VERY EXTENSIVE. Molarity Calculators include:
Volume from Mass & Concentration Calculator; Molarity from Mass & Volume Calculator; Dilute a Stock Solution Calculator..." 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
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 "...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
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 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..." 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 Calculator input values include:
Standardised Molecular Formula; Molecular Ion Isotope Pattern..." MOLECULAR WEIGHT CALCULATOR (JAVA APPLET) - ChemicalLogic Molecular Weight Calculator input values include:
MOLECULAR WEIGHT CALCULATION - Institut für Chemie (Institute of Chemistry), Freie Universität Berlin, Germany VERY EXTENSIVE. Molecular Weight Calculator input values include:
Elemental Analysis; Double Bond Equivalents..." RNA MOLECULAR WEIGHT CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
PROTEIN MOLECULAR WEIGHT CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PROTEIN MOLECULAR WEIGHT CALCULATOR - S. Venkataraman, Michigan State University VERY EXTENSIVE. Protein Molecular Weight Calculator input values include:
Distance of First Marker; Distance of Second Marker; Distance of Unknown; etc..." |
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 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
Mirek's Java Cellebration (MJCell) is "...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...") Greenberg-Hastings Models Greenberg-Hastings (GH) Model "...is perhaps the simplest CA prototype for an excitable medium..." 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
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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
Oligonucleotide Mass Calculator "...calculates also electrospray series, CID fragments, endo- and exonuclease fragments. Includes the possibility for calculating modified residues..." Oligo Composition Calculator Oligo Composition Calculator "...Finds nucleotide compositions from a given mass. User defined residues can be included..." Oligonucleotide
MONGO OLIGO MASS CALCULATOR - J.A. McCloskey, P.F. Crain, & J. Rozenski, Huntsman Cancer Institute, University of Utah VERY EXTENSIVE. Oligonucleotide Mass Calculator "...calculates also electrospray series, CID fragments, endo- and exonuclease fragments. Includes the possibility for calculating modified residues..." 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 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 input values include: "...Enter Oligonucleotide Sequence...Enter Number of Fluorescent tags per strand..." For more information see Basic Sciences |
ACCURATE MASS & PEPTIDE MODIFICATION ACCURATE MASS & PEPTIDE MODIFICATION - A. Bohne-Lang, Molecular Modeling, Central Sectroscopy Department, German Cancer Research Center (DKFZ), Heidelberb, Germany VERY EXTENSIVE. Peptide Accurate Mass Calculator & Peptide Modification Calculator can "...help to unravel information encrypted in the deltamass value of accurate peptide masses. Deltamass is the post-decimal-point part of the accurate mass..." For more information see the Andreas Bohne-Lang's Home Page or the Central Sectroscopy Department - Molecular Modeling PEPTIDE MASS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
Peptide Mass Calculator: "...work out the mass of your amino acid sequence..." 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:
Calculate Molecular Mass, [M+H]+, ES Series Positive Mode or ES Series Negative Mode; using Average Masses or Monoisotopic Masses..." PEPTIDE MASS - ExPASy Molecular Biology Server, Geneva University Hospital and the University of Geneva VERY EXTENSIVE. Peptide Mass Calculator "...also returns theoretical isoelectric point and mass values for the protein of interest. If desired, PeptideMass can return the mass of peptides known to carry post-translational modifications,..." Peptide Mass Calculator input values include:
Peptide Masses are: cysteines treated with, with acrylamide adducts, with methionines oxidized, etc..." |
Examples of Prowl Tools & Calculators include:
EXPASY PROTEOMICS TOOLS - ExPASy Molecular Biology Server, Geneva University Hospital and the University of Geneva VERY VERY VERY...EXTENSIVE. For more information see ExPASy Molecular Biology Server
Aldente "...a tool to identify proteins from peptide mass fingerprinting data..." GlycoMod GlycoMod "...a tool that can predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses..." FindPept FindPept "...can identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications..." BRADFORD TEST BY REGRESSION ANALYSIS
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
Protein Molecular Weight Calculator input values include:
Distance of First Marker; Distance of Second Marker; Distance of Unknown; etc..." |
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 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 |
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
[GdmCl] AND [UREA] CALCULATORS & APPLETS
[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
[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 |
PEPFRAG CALCULATORS & APPLETS
PROTEIN PROSPECTOR CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
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