Molecular
The Python Macromolecular Library (mmLib) is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language. It is accessed via a layered, object-oriented application programming interface, and...
Platforms: Windows, Mac, *nix, Python, BSD Solaris
License: Freeware | Download (58): The Python Macromolecular Library Download |
Matlab procedure that generates a Surface Plasmon Resonance profile to compare it with experimental data. Relevant parameters are given as graphical input.A 90dlT- prism is assumed, the reflected intensity is plotted against the external angle. It can be plotted on its own, or compared to a file...
Platforms: Matlab
License: Freeware | Size: 10 KB | Download (45): Surface Plasmon Resonance Calculator Download |
HOT is a package originally constructed for combustion modeling in Matlab. It calculates common thermodynamic properties such as enthalpy, specific heat, entropy, internal energy, gamma, ideal gas constant, molecular weight, etc
Platforms: Matlab
License: Freeware | Size: 143.36 KB | Download (40): HOT Thermodynamic Tools for Matlab Download |
MolMass is a function for calculating the molar weight of a substance given in form of a chemical formula.Function call: MM = MolMass(substance)Substance is a string of the chemical formula of a substance.Example: MM = MolMass('Fe2(SO4)3');Substance can also be a vector of substances opened by...
Platforms: Matlab
License: Freeware | Size: 102.4 KB | Download (46): Molecular Weight Calculator Function Download |
The Mole Package contains 3 mfiles and 1 matfile. molecules2 calculates molecular masses pertable provides data on the elements sym2an converts a chemical symbol to a valid atomic number (useful for molecules2 and pertable). atoms contains atomic number data.
Platforms: Matlab
License: Freeware | Size: 10 KB | Download (49): Mole Package Download |
This function allows calculating the compressibility factor, the coefficient of fugacity and density of a pure compound using the modified Iwai-Margerum-Lu Cubic Equation of State (IML-CEoS).The next data are necessary: temperature, pressure, molecular weight, acentric factor, and experimental...
Platforms: Matlab
License: Shareware | Cost: $0.00 USD | Size: 10 KB | Download (39): Iwai-Margerum-Lu Cubic Equation of State Download |
This function allows calculating the compressibility factor, the coefficient of fugacity and density of a pure compound using the Soave-Benedict-Webb-Rubin equation of state (SBWR-EOS).The next data are necessary: temperature, pressure, molecular weight, acentric factor, and critical properties...
Platforms: Matlab
License: Shareware | Cost: $0.00 USD | Size: 10 KB | Download (49): Soave-Benedict-Webb-Rubin Equation of State Download |
Molecular Workbench simulation of a polypeptide crystal. Use the slider in the top right to increase the temperature of the system until the polypeptides lose their original form. Cool the system. Why don't the polypeptides regenerate their original forms?
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 1.02 KB | Download (44): Pressure on water Download |
SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView reads and writes various file formats of DNA and protein sequences and of phylogenetic trees. SeaView drives programs muscle or clustalw for multiple sequence alignment, and...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 3.71 MB | Download (45): SeaView fopr Mac Download |
NCL is a C++ library for interpreting data files created according to the NEXUS file format used in molecular evolution and phylogenetic systematics.
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 1.07 MB | Download (41): NCL Download |
Seqlib is a Python module and application package for population genetics (and more). It allows processing, analyzing and simulating biological sequences. It is specifically designed for automated large-scale sequence analysis. Main features: * Fasta-centered input and output, format...
Platforms: Mac
License: Freeware | Size: 2.7 MB | Download (37): SEQLIB Download |
MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber. It allows one to read molecular dynamics trajectories and access the atomic coordinates through numpy arrays. This provides a flexible and relatively...
Platforms: Mac
License: Freeware | Size: 19.01 MB | Download (42): MDAnalysis Download |
How do you know if a chemical equation is balanced? What can you change to balance an equation? Play a game to test your ideas! Sample Learning Goals * Balance a chemical equation. * Recognize that atoms are conserved in a chemical reaction. * Describe the difference between coefficients and...
Platforms: Mac
License: Freeware | Size: 1.37 MB | Download (35): Balancing Chemical Equations Download |
Ridom TraceEdit is a cross-platform graphical DNA trace viewer and editor. TraceEdit displays the chromatogram files from Applied Biosystems automated sequencers and files in the Staden SCF format. Incorrect base calls can be edited and saved. TraceEdit is freely available and designed to operate...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 5.72 MB | Download (35): Ridom TraceEdit Download |
jMOTU is a software package for clustering barcode DNA sequence data into molecular operational taxonomic units (MOTU). If you are not sure what a MOTU is, please see the DNA Barcoding pages on our website. jMOTU does the following: *reads input sequences in FASTA or NEXUS format *calculates...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 7.15 MB | Download (78): jMOTU Download |
ABNER is a software tool for molecular biology text analysis. It began as a user-friendly interface for a system developed as part of the NLPBA/BioNLP 2004 Shared Task challenge. The details of that system are described in the paper below (Settles, 2004). At ABNER's core is a statistical machine...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 9.5 MB | Download (37): ABNER Download |
Toxtree is a full-featured and flexible user-friendly open source application, which is able to estimate toxic hazard by applying a decision tree approach. Toxtree could be applied to datasets from various compatible file types. User-defined molecular structures are also supported - they could...
Platforms: Mac
License: Freeware | Size: 55.79 MB | Download (36): Toxtree Download |
The PSI3 suite of quantum chemical programs is designed for efficient, high-accuracy calculations of properties of small to medium-sized molecules. The package's current capabilities include a variety of Hartree-Fock, coupled cluster, complete-active-space self-consistent-field, and...
Platforms: Mac
License: Freeware | Size: 7.07 MB | Download (36): PSI3 Download |
Did you ever imagine that you can use light to move a microscopic plastic bead? Explore the forces on the bead or slow time to see the interaction with the laser's electric field. Use the optical tweezers to manipulate a single strand of DNA and explore the physics of tiny molecular motors. Can...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 1.47 MB | Download (33): Optical Tweezers and Applications Download |
What happens when sugar and salt are added to water? Pour in sugar, shake in salt, and evaporate water to see the effects on concentration and conductivity. Zoom in to see how different sugar and salt compounds dissolve. Zoom in again to explore the role of water. Teaching Resources Main...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 3.94 MB | Download (35): Sugar and Salt Solutions Download |