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List of Applications

ITEM

APPLICATION

USAGE

APPLICATION AREAS

1

MATLAB

Use for algorism development, data visualization, data analysis and senior technology computing language and interactive environment of numerical calculation

Math and computation, Algorithm development.

Modeling, simulation, and prototyping, Data analysis, exploration, and visualization, Scientific and engineering graphics, Application development, including Graphical User Interface building.

2

Mathematica

One set of scientific computing software which combines numeric and symbolic calculation engine, graphic system, programing language and text system.

Comprehensive Image Processing Environment,

Graphs and Networks Modeling, Graphs and Networks Analysis’, Integrated Control Systems Design, Integrated Wavelet Analysis, Built-in Financial Computations, Import and Export Formats

 

3

Red Hat linux

Operating system

 

4

Discovery Studio

New molecular modeling environment, professional life science molecular simulation software

Molecular MechanicsMolecular DynamicsQuantum Mechanics, Simulations, Ligand Design, Macromolecule design and validation, Macromolecule engineering

5

Dock

Molecular docking software

Bi0-infomatics, Drug Discovery

6

Autodock

Molecular couple rings software package

Structure-based Design, Lead Optimization, Virtual Screening, protein-protein docking, chemical mechanism, Drug Discovery, Bio-informatics

7

Modeller

Isogeny or comparative protein three dimensional
structure modeling software 

Bio-informatics

8

BWA

Sequencing adjustment read software of large reference genome 

Computational Chemistry

9

BLAST

Protein database or DNA database similarity comparison and analysis tool

Bioinformatics,

10

MPIBLAST

Parallel sequence alignment software

 

11

FASTA

Database similarity searching program

Bioinformatics

12

Velvet

Short sequence assembly tool. Velvet is a de novo genomic assembler specially designed for short read sequencing technologies. Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.

Bioinformatics

13

Gromacs

Molecular dynamics general software package,
imitate particles system Newton motion formula

Computational chemistry research

14

NAMD

Simulate parallel molecule dynamics code of macromolecule system, and calculate atom track. NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. Simulation preparation and analysis is integrated into the visualization package.

molecular dynamics simulation-computational chemistry

15

CHARMM

Molecule dynamics software, conduct classical, quantum or quantum classical hybridization simulation. A molecular simulation program with broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques including QM/MM, MM/CG, and a range of implicit solvent models. 

► CHARMM primarily targets biological systems including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments. CHARMM also finds broad applications for inorganic materials with applications in materials design.

Bioinformatics and computational chemistry

16

LAMMPS

Large-scale atomic and molecular parallel simulator. has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

Engineering, electrical and mechanical usage

17

VMD

Molecule visualization program, apply 3D graphic and built-in script to display large-scale molecular system, animation production and analysis.

Molecule visualization in computational chemistry and bioinformatics

18

ARP/wARP

Macromolecular modeling software.It is  macromolecular model automatically, with a reproducible computational procedure

Structural genomics, X-ray crystallography, software, model building, ligand placement

19

Cns

Macromolecular structure research software

Computational Chemistry

20

X!tandem

Proteomics database retrieval software

Protein identification.

22

EMAN

Single particle refactoring software

Structural Analysis

23

IDL

Data analysis and graphic application program and programing language, which can transform data into graphics, and enhance analysis and understanding

Statistical Analysis

24

Tecplot

Visualization software, to map and generate animation based on data and conduct analysis on complicated data, make multiple layout arrangement, and form relevance of outcome, graphics and animation.

Computational Fluid Dynamics

25

Origin

Graphics visualization and data analysis software is a common senior data analysis and mapping tool by scientific researchers and engineers.

Scientific Graphing

26

WRF

Weather research and forecast system model

Weather Forecasting and Climate Modelling

27

MM5

Mesoscale numerical forecast model

Weather Forecasting and Climate Modelling

28

CCSM

Unifying weather system model. It is a complete coupling model research system combines atmosphere, ocean, land and sea ice.

Weather Forecasting and Climate Modelling

29

Gaussian

Quantum chemistry software package, forecast period system energy, structure and molecular track.

Computational Chemistry

30

Dacapo

Java benchmark test tool

Computational Chemistry

31

Abinit

Based on density functional theory, apply pseudo potential and plane wave vector method to deal with electron and nuclear constituting system.

Computational Chemistry; Materials Science

32

CPMD

First principle molecular dynamics method, which applies pseudo potential, plain wave basic vector and density functional theory (DFT), calculates applied force between atoms (molecules).

Computational Chemistry; Molecular Dynamics

33

Materials Studio

Simulating software of material science field.
Convenient to set up three-dimensional structure model, target on all crystals, amorphous and macromolecular material quality and related process.

Computational Chemistry; Materials Science

34

VASP

Apply pseudo potential and plain wave basic vector.
Software package to conduct calculation from quantum dynamics and molecular dynamics. 

Computational Chemistry; Molecular Dynamics

35

WIEN2K

Apply density functional theory to calculate electronic structure of solid.

Computational Chemistry

36

TURBOMOLE

Quantum chemistry computing software, rapidly and stably deal with industrial application molecule.

Computational Chemistry; Quantum Chemistry

37

Siesta

Use for simulation of molecule and solid electronic structure calculation and molecular dynamics.

Computational Chemistry; Molecular Dynamics; Materials Science

38

Ansys

Large-scale general software of finite element analysis that integrates structure, fluid, electric field and sound field analysis.

Computational Chemistry; Engineering Simulation

39

CFX

General computing dynamics software based on partition structuring and control volume method.

Computational Chemistry; Computational Fluid Dynamics

40

Fluent

Fluid dynamics software

Computational Fluid Dynamics ; Computational Chemistry

41

FDS

Fluid dynamics calculation model, emphasize on smoke flow and thermal transmission study.

Computational Chemistry; Materials Science

42

Phaser

General simulating toll for dynamic system, suit for graph and numeric simulation analysis of difference/difference equation.

Statistical analysis

43

Shirondiger Suite

 Chemical simulation software for use in pharmaceutical, biotechnology, and materials research.

Computational chemistry – Drug discovery

44

Pymol

Stunning high-performance molecular graphics for communicating structural results

Bioinformatics -DNA analysis

45

Chimera

 Highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, 

Bioinformatics -DNA analysis

46

Jmodeltest

A Java-enabled application that can help scientists to analyze nucleotide substitutions, with up to five model. Application that can perform a selection of nucleotide substitutions, useful in DNA analysis, with support for large packets of data.

Bioinformatics -DNA analysis

47

Figtree

FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures.

Bioinformatics

48

Sparks

Engine for large-scale data processing that performs in-memory computing. Spark offers bindings in Java, Scala, Python and R for building parallel applications.

Statistical Analysis

49

Phyml

Phyml estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. Phyml offers a large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches.

Bioinformatics

50

DataWarrior

Cheminformatics Program for Data Visualization and Analysis. DataWarrior combines dynamic graphical views and interactive row filtering with chemical intelligence

Computational chemistry

51

FreeFem++

Allows the resolution of partial differential equation using the finite element method.

Statistical Analysis

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