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MARTINDALE’S CALCULATORS ON-LINE CENTER BIOSCIENCE & BIOTECHNOLOGY (Calculators, Applets, Spreadsheets, |
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ANALYTICAL ULTRACENTRIFUGATION CALCULATORS & SOFTWARE
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.
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…” AXON POTENTIAL CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
interactions, current injection, voltage clamping, effects of changing equilibrium potentials, and effects of channel blocking drugs…” For more information see
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 FOR BOTANY RELATED CENTERS WITH CALCULATORS, COURSES, DATABASES, ETC. SEE THE BOTANY CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
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 BOTANY CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
Plant Pattern Formation…” For more information see
Cylinder Lattices Applet Cylinder Lattices Applet
possible spiral lattices and their organization according to their divergence angles, expansion rate, and parastichy numbers…”
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 CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
BIS-TRIS; Boric Acid; CABS; CAPSO; Citric Acid; DIPSO; DIPSO Sodium Salts; Ethanolamne; Glycolic Acid; HPEBS; HEPES; IMDAZOLE; etc…” For more information see BUFFER CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
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:
Pyridine; Bis-tris; ADA; PIPES; ACES; Phosphate; Tricine; etc…” Volume; pH; Concentration; Control of Ionic Strength; For more information see CITRIC ACID CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
PHOSAPHATE BUFFER CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
necessary to achieve a buffer at a given pH and strength…” For more information see
monosodium phosphate and trisodium phosphate necessary to achieve a buffer at a given pH and buffer strength…”
monosodium phosphate and disodium phosphate necessary to achieve a buffer at a given pH and buffer strength…” CARBOHYDRATES RELATED CENTER FOR CARBOHYDRATES SEE THE
CELL CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
For more information see
between directional vectors [uvw] and the normals of planes (hkl). Their directions are identical for the cubic system…” For more information see ELECTROPHYSIOLOGY CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
basics of the initiation and propagation of the nerve impulse using equivalent circuits…” Nerve Impulse Laboratory Manual
“…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:
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
the three main conductances of the squid giant axon. The conductances are shown as variable resistor, the reversal potentials…”
and idealized cartoon of three of the four S4 segments and the inactivating particle of the sodium channel…”
propagation of the action potential by solving the Hodgkin and Huxley (HH) model for the space-clamped…”
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 the |
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CENTRIFUGE CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
CENTRIFUGE K-FACTOR CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
Radius Minimum & Maximum; Maximum Rotor Speed; etc…” For more information see
Radius Minimum & Maximum; Maximum Rotor Speed; Calculate for either RPM, RCF Average, RCF Maximum, or k-Factor…” For more information see COGNITION CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
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
show that item length (or word length) effects could be obtained in a model that does not include any rehearsal…”
As in the experiment, the model is then told what the correct response was. On the second trial, it decides whether the current stimulus is smaller (or lower in frequency, or shorter in length) than the previous stimulus. If it is smaller, then…”
of serial learning. This simulation implements his model….” CHEMICAL SOLUTIONS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
VIRTUAL LABORATORIES CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS PROTOCOLS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
at Max-Planck-Institut fur Molekulare Genetik…” Available in English, German/Deutsch, Russian & Ukrainian. Examples of “Molecular Biology” Calculators Subject Categories include
Laboratory Buffer Calculators; Single Component Solution Calculators; Compound Solution Calculators; Antibiotic Solution Calculators; etc…” For more information see
Preparation of Stock Solutions for Ampicillin Calculator; Preparation of Stock Solutions for Carbenicillin Calculator; Preparation of Stock Solutions for Chloramphenicol Calculator; etc..”
Betaine Calculator; EDTA Calculator; EtBr Calculator; Gelatin Calculator; HEPES Calculator; PEGV; Sucrose Calculator; etc. Acids and Alkalis Calculators;
Loading Buffer Calculator; Bacteriophage Lambda Buffer Calculator; Denaturation Buffer Calculator; Neutraliszation Buffer Calculator; Plasmid Solution Calculator; Oligonucleotide Gel Staining Mix Calculator; etc…”
acids according to their optical density: DNA, RNA, Oligonucleotides,…”
electro-competent cells and protein expression. The program may be used also for other organisms in the logarithmic stage of growth…”
primers and nucleotides for optimal PCR reaction and the necessary number of cycles…”
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PCR CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
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
(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
allowing the user to analyze primers over the Internet…” For more information see
needed to do two-dimensional box titrations of various reactants in polmerase chain reactions…” For more information see DNA FRAGMENT SIZE CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
relationship between molecular weight and distance migrated…” For more information see ELECTROPHORESIS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
size when direct current is applied to the ends of an electrophoresis gel…” For more information see
ELECTROPHORESIS SIMULATION OF DNA – CALCULATORS & APPLETS
ELECTROPHORESIS SIMULATION OF PROTEINS
the applet will plot the result and determine the experimental molecular weight of the unknowns…” For more information see FRAGMENT SIZE CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
relationship between molecular weight and migration…” For more information see GEL ELECTROPHORESIS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
30% Polyacrylamide; 10% Ammonium persulfate; 10% SD; etc…” For more information see |
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GENETICS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
GENETIC COURSES WITH CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
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 EYE COLOR CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
the inheritance of human eye color…” For more information see
POPULATION GENETICS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
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
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
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GENE REGULATION CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
PROKARYOTIC DATABASE OF GENE REGULATION AND REGULATORY NETWORKS
networks in prokaryotes with focus on transcriptional regulation…” PRODORIC includes:
Proteins (Transcriptional Regulators); Binding Sites; Alphabetical Regulon List; Matrix and Consensi; Chemical Reaction; Possible Pathways; Regulated Compound…”
single or composite DNA patterns. It was especially designed to analyze transcription factor binding sites in…”
tool for predicting signal peptide sequences and their cleavage positions in bacterial and eukaryotic proteins…” |
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METABOLIC ENGINEERING CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
stable isotope and radioisotope tracer kinetics in terms of metabolic fluxes and compartmentation of pools…” For more information see
MOLECULAR BIOLOGY CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
at Max-Planck-Institut fur Molekulare Genetik…” Available in English, German/Deutsch, Russian & Ukrainian. Examples of “Molecular Biology” Calculators Subject Categories include
Laboratory Buffer Calculators; Single Component Solution Calculators; Compound Solution Calculators; Antibiotic Solution Calculators; etc…” For more information see
Preparation of Stock Solutions for Ampicillin Calculator; Preparation of Stock Solutions for Carbenicillin Calculator; Preparation of Stock Solutions for Chloramphenicol Calculator; etc..”
Betaine Calculator; EDTA Calculator; EtBr Calculator; Gelatin Calculator; HEPES Calculator; PEGV; Sucrose Calculator; etc. Acids and Alkalis Calculators;
Loading Buffer Calculator; Bacteriophage Lambda Buffer Calculator; Denaturation Buffer Calculator; Neutraliszation Buffer Calculator; Plasmid Solution Calculator; Oligonucleotide Gel Staining Mix Calculator; etc…”
acids according to their optical density: DNA, RNA, Oligonucleotides,…”
electro-competent cells and protein expression. The program may be used also for other organisms in the logarithmic stage of growth…”
primers and nucleotides for optimal PCR reaction and the necessary number of cycles…”
MOLECULAR BIOLOGY CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
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
the easy opportunity to derive a considerable amount of useful information from nucleotide or protein sequence data…” For more information see the |
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MOLECULAR MASS, EXACT MASS, ELEMENTAL ANALYSIS CALCULATORS & APPLETS
Exact Mass, Elemental Analysis and Plots the Isotopic Distribution Graph… For more information see MOLAR MASS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
Volume from Mass & Concentration Calculator; Molarity from Mass & Volume Calculator; Dilute a Stock Solution Calculator…” For more information see
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
to calculate molar mass and elemental composition…” For more information see MOLECULAR MASS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS MOLECULAR WEIGHT CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
MOLECULAR FORMULA FROM A HRMS WEIGHT CALCULATORS & APPLETS
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 MOLECULAR WEIGHT CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
Molecular Weight Calculator OUTPUT Values include:
Molecular Weight; Element Percentage; Standardised Molecular Formula; Molecular Ion Isotope Pattern…” For more information see
Molecular Weight Calculator OUTPUT Values include:
Physical Molecular Weight; Elemental Analysis; Double Bond Equivalents…” For more information see the RNA MOLECULAR WEIGHT CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
PROTEIN MOLECULAR WEIGHT CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
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
Single-Stranded DNA Molecular Weight Calculator; Double-Stranded DNA Molecular Weight Calculator; RNA Molecular Weight Calculator; etc…” For more information see |
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ARTIFICIAL LIFE CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
NEURAL NETWORKS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
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…”
show that the Life Without Death rule is capable of emulating Boolean circuits…”
NEURAL NET CONCEPTS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS |
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OLIGONUCLEOTIDE CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS OLIGONUCLEOTIDE PROPERTIES CALCULATORS & APPLETS
PEPTIDE MASS CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
handles n-terminal modifications, oxidized cysteines and phosphorylated amino acids…” For more information see
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 |
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PROTEIN CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
collections with peptide mass maps…” ProteinInfo
of protein sequences…” PeptideMap
sequences…” PepFrag
sequences that matches a single tandem mass spectrum…” X! Tandem
peptide sequences that matches tandem mass spectra…” X! Hunter; GPMDB; etc…” For more information see
PROTEIN MOLECULAR WEIGHT CALCULATORS & APPLETS
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
Single-Stranded DNA Molecular Weight Calculator; Double-Stranded DNA Molecular Weight Calculator; RNA Molecular Weight Calculator; etc…” For more information see
PER RESIDUE SOLVENT ACCESSIBLE SURFACE CALCULATORS & APPLETS
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 HOMOLOG FINDER
find the homolgous residues in any other proteins in the main alignment…” For more information see PROTEIN FOLDING CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
macromolecules (such as RNA). Associated with it are a variety of free software tools for structural analysis…” For more information see the [GdmCl] AND [UREA] CALCULATORS & APPLETS
For more information see PROTEIN IDENTIFICATION CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
PEPFRAG CALCULATORS & APPLETS
from a collection of sequences that matches a single tandem mass spectrum…” For more information see PROTEIN PROSPECTOR CALCULATORS, APPLETS, ANIMATIONS & SIMULATIONS
PROTEIN TRANSCRIPTION AND TRANSLATION CALCULATORS & APPLETS
For more information see |
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