What Runs Where on Athena: Simulation & Modeling

Title and Description:

AFNI
Description: collection of programs for viewing and analysing functional magnetic resonance images of the brain. Supplied with many associated command-line utility functions

TO RUN:

athena% add seven

athena% afni data-directory (main application)

athena% command options files (utilities)

Please see documentation for usage of utility commands

Local documentation starts here; there is also a central information site and a resource site

See also: clustalw, GENSCAN, NetPBM Utilities, xv

Title and Description:

Biopython
Description: collection of Python tools for computational molecular biology- allows processing of biological sequences and databases

To run in interactive mode:

athena% add seven

athena% biopython

followed by commands from the Biopython package, for example:

>>> from Bio.Seq import Seq

>>> new_seq = Seq('GATC')

>>> new_seq[0:2]

To run as a stand-alone application, you can write python scripts that contain Biopython commands

There is a documentation site

See also: BLAST, CLC Free Sequence Viewer , clustalw, emboss, Geneious, GENSCAN, hmmer, meme/mast, Osprey, phylip, primer3, python

Title and Description:

BLAST
Description: BLAST (Basic Local Alignment Search Tool) is an application for finding regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. BLAST can be run standalone, as an NCBI Web client, via a local BLAST server and via a Web form at the NCBI Web site. This installation contains the standalone and Web client versions from NCBI

TO RUN:

athena% blastcl3 -i query options > outfile (Web client: to run query query, with output in outfile)

athena% formatdb -i data options (standalone: to index a database data)

athena% program options -d data -i query > outfile (standalone: use program to run query query against database data, output in outfile)

There is documentation, an NCBI tutorial, Wiki and a Web page

See also: Biopython, CLC Free Sequence Viewer , clustalw, emboss, Geneious, GENSCAN, hmmer, meme/mast, phylip, primer3

Title and Description:

CLC Free Sequence Viewer
Description: tool for bioinformatics analysis including: alignment creation and editing, interactive restriction site analysis, phylogenetics, integrated GenBank searches, DNA to protein translation and other features

TO RUN:

athena% add clcbio

athena% clcseqview4 &

There is a local 4.6.1 pdf manual and Web site

See also: Biopython, BLAST, clustalw, emboss, Geneious, GENSCAN, hmmer, meme/mast, Net Entrez, phylip

Note:

This application has been renamed from CLC Free Workbench to CLC Free Sequence Viewer

Title and Description:

clustalw
Description: general purpose multiple sequence alignment program for DNA or proteins

TO RUN:

athena% add clustalw

athena% clustalw

There is local documentation here, here and here; also a Web page

See also: AFNI, Biopython, BLAST, CLC Free Sequence Viewer , emboss, Geneious, GENSCAN, hmmer, meme/mast, phylip, primer3

Title and Description:

emboss
Description: the European Molecular Biology Suite is a large collection of tools for molecular analysis of genomic data. It can handle data in a variety of formats and allows transparent retrieval of sequence data from the Web. A GUI Java-based interface, jemboss, is also available. emboss is configured to use clustalw, hmmer, meme and primer3 as helper applications. Most programs in the optional EMBASSY suite have also been installed. Graphics output is possible via Plplot libraries included in the installation

TO RUN:

Athena machine:

athena% setup emboss

athena% jemboss (to run GUI)

athena% command options file(s) (command is one of the emboss commands; see docs for list)

Linux machine running OpenAFS client:

$ csh

$ attach emboss

$ source /mit/emboss/.attachrc

athena% jemboss (to run GUI)

athena% command options file(s) (command is one of the emboss commands; see docs for list)

There is local documentation, a tutorial and quick reference, documentation at the development site and a Web page

See also: Biopython, BLAST, CLC Free Sequence Viewer , clustalw, Geneious, GENSCAN, hmmer, meme/mast, phylip, primer3

Note:

this is an older release which will not be updated. Users can install current versions in Ubuntu packages using aptitude or synaptic

Title and Description:

Geneious
Description: integrated bioinformatics tool suite for manipulating, finding, sharing and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information and publications

TO RUN:

athena% add geneious

athena% geneious &

There is a local pdf manual, and Web site

See also: Biopython, BLAST, CLC Free Sequence Viewer , clustalw, emboss, GENSCAN, hmmer, meme/mast, Net Entrez, phylip

Title and Description:

GENSCAN
Description: tool for predicting the locations and exon-intron structures of genes in genomic sequences

TO RUN:

athena% add seven

athena% genscan /mit/seven/share/HumanIso.smat sequence-file options (vertebrates)

athena% genscan /mit/seven/share/Maize.smat sequence-file options (maize)

athena% genscan /mit/seven/share/Arabidopsis.smat sequence-file options (arabidopsis)

Local documentation starts here

See also: AFNI, Biopython, BLAST, CLC Free Sequence Viewer , clustalw, emboss, Geneious, hmmer, meme/mast, phylip

Title and Description:

hmmer
Description: set of tools that profile hidden Markov models for protein sequence analysis. This can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus

TO RUN:

athena% hmmfetch options database name

athena% hmmalign options hmmfile seqfile

athena% hmmsearch options hmmfile seqfile

athena% hmmbuild options hmmfile seqfile

(see man hhher for documentation)

There is local documentation and a Web page

See also: Biopython, BLAST, CLC Free Sequence Viewer , clustalw, emboss, Geneious, GENSCAN, meme/mast, phylip, primer3

Title and Description:

meme/mast
Description: meme is a tool for discovering motifs in a group of related DNA or protein sequences. mast is a tool for searching molecular sequence databases for sequences that contain one or more of a group of known motifs. A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences

TO RUN:

athena% add meme

athena% meme dataset options

athena% mast motif-file options

There is local documentation for meme and mast; there is also a Web page

See also: Biopython, BLAST, CLC Free Sequence Viewer , clustalw, emboss, Geneious, GENSCAN, hmmer, phylip, primer3

Title and Description:

NEURON
Description: simulator of neurons and networks of neurons, with an extensible library of biophysical mechanisms

TO RUN:

athena% add neuron

athena% nrngui (to run GUI)

athena% neurondemo (to run a demo)

Look below /mit/neuron/bin to see launch commands for various components and utilities; local tutorials and documentation are available. There is an author Web page and pointers to additional documentation

See also: Osprey

Title and Description:

Osprey
Description: tool for graphically representing biological interaction networks, drawing on data from various interaction databases. Osprey is integrated with the BioGRID

TO RUN:

athena% add osprey

athena% osprey &

There is an author page with documentation

See also: Biopython, NEURON

Note:

Sun version not supported by authors and has some format/sizing problems; windows may need to be enlarged manually to see all dialog buttons (in particular, initital launch "Select database.." dialog); help browser won't launch on help invocation

Title and Description:

phylip
Description: phylip (Phylogeny Inference Package) is a collection of separate programs for inferring phylogenies (evolutionary trees). It can infer phylogenies by parsimony, compatibility, distance matrix methods and likelihood. It can also compute consensus trees, compute distances between trees, draw trees, resample data sets by bootstrapping or jackknifing, edit trees and compute distance matrices. It can handle data that are nucleotide sequences, protein sequences, gene frequencies, restriction sites, restriction fragments, distances, discrete characters and continuous characters.

TO RUN:

athena% add phylip

athena% command file(s) (command is one of the phylip commands; see docs for list)

generally a data file named intree or infile is expected as input in the current directory; output is produced in files outtree and outfile in the same directory. drawree and drawgram additionally require a font file in the current directory; a number are supplied with the distribution, and a suitable one can be copied from the /mit/phylip_v3.66/fonts directory to the current directory and renamed to fontfile

There is local documentation and a Web page

See also: Biopython, BLAST, CLC Free Sequence Viewer , clustalw, emboss, Geneious, GENSCAN, hmmer, meme/mast, primer3

Note:

this application is no longer installed. You can install it from the phylip Ubuntu package using aptitude or synaptic

Title and Description:

primer3
Description: program for designing Polymerase Chain Reaction primers. It can also design hybridization probes and sequencing primers

TO RUN:

athena% primer3_core < inputdata

There is an author page and documentation

See also: Biopython, BLAST, clustalw, emboss, hmmer, meme/mast, phylip

Note:

this application is no longer installed. You can install it from the primer3 Ubuntu package using aptitude or synaptic

Title and Description:

CalculiX
Description: 3d structural analysis finite-element program, incorporating a pre- and post-processor (Graphix, cgx) and solution engine (CrunchiX, ccx_1.6). A vda to fdb conversion utility is also in the locker

TO RUN:

athena% add calculix

athena% ccx_1.6 file (to run ccx_1.6 on model file file.inp)

athena% cgx model.frd (to view model in file model.frd; use left mouse button outside drawing rectangle for popup menu)

athena% cgx -b model.fbd (to preprocess model in file model.fbd; use left mouse button outside drawing rectangle for popup menu)

athena% vda2fbd file.vda > file.fbd (to convert file.vda to file.fbd)

There is an online ccx manual, cgx manual, cgx tutorial and an author Web page; there is also a discussion group

See also: adina, Elmer, FreeFem++, Mathematica (IMTEK Mathematica supplement), OpenFOAM

Title and Description:

EasyMesh
Description: 2d Delaunay mesh generator that supports a variety of features, including materials containing holes, domains composed of more than one material and Laplacian smoothing. Output can be generated in a variety of file formats. ShowMesh is a viewer for displaying meshes created by EasyMesh

TO RUN:

athena% add easymesh

athena% easymesh infile options (to run EasyMesh on input data file infile)

athena% showmesh infile (to run ShowMesh on input data file infile)

There is EasyMesh documentation, ShowMesh documentation and an author Web page

EasyMesh is used by some of the demos in the IMTEK Mathematica supplement added to our Mathematica installation

See also: Mathematica, tetgen, triangle

Title and Description:

Elmer
Description: multiphysics/finite-element application capable of solving problems that can be described by partial differential equations in fields such as fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics. It includes a front end, solver and post-processor, and can import data from a variety of commercial finite-element applications

TO RUN:

athena% add elmer

athena% ElmerFront (to run front end)

athena% ElmerSolver (to run solver on model file file.sif, where this file is in the current directory)

athena% ElmerPost (to run post-processor; needs to read data in file.ep generated by solver)

There is local pdf documentation and a Web page

See also: CalculiX, FreeFem++, Mathematica (IMTEK Mathematica supplement, maxwell, OpenFOAM

Title and Description:

FreeFem++
Description: 2d finite-element method solver for partial differential equations that incorporates an internal scripting language. The distribution comes with an IDE and can output graphics directly

TO RUN:

athena% add freefempp

athena% FreeFem++ file.edp (to run FreeFem++ on model file file.edp)

athena% FreeFem++-ide & (to launch the IDE)

There is an online manual and an author Web page

See also: CalculiX, Elmer, Mathematica (IMTEK Mathematica supplement), maxwell, OpenFOAM

Title and Description:

OpenFOAM
Description: OpenFOAM is primarily a C++ library used to create executables, known as applications. The applications fall into two categories: solvers, that are each designed to solve a specific problem in continuum mechanics; and utilities, that are designed to perform tasks that involve data manipulation. The OpenFOAM distribution contains numerous solvers and utilities covering a wide range of problems. New solvers and utilities can be created by its users with some prerequisite knowledge of the underlying method, physics and programming techniques involved. Information relating to these subjects is in the Programmer's Guide. OpenFOAM is supplied with pre- and post-processing environments. The interfaces to the pre- and post-processing are themselves OpenFOAM utilities

TO RUN:

athena% setup openfoam

athena% FoamX (to run GUI setup interface)

athena% paraFoam root case (to run postprocessor/display utility on a specific case rooted at root)

Many utilities and solvers can be run directly from the command line.

There is a local User Guide, a home page with html documentation, and a Wiki

See also: CalculiX, Elmer, FreeFem++, Mathematica (IMTEK Mathematica supplement), maxwell

Title and Description:

tetgen
Description: 3d tetrahedral mesh generator and Delaunay triangulator. These meshes can be used in finite-element and finite-volume simulations. tetview is a 3d viewer for viewing meshes created by tetgen as well as other objects and triangular and tetrahedral meshes in other formats

TO RUN:

athena% add tetgen

athena% tetgen options infile (to run tetgen on input data file infile)

athena% tetview options infile (to run tetview on input data file infile) (currently broken on debathena machines)

There is a pdf manual and author site

tetgen is used by some of the demos in the IMTEK Mathematica supplement added to our Mathematica installation

See also: EasyMesh, Mathematica, triangle

Title and Description:

triangle
Description: 2d mesh generator and Delaunay triangulator that supports a variety of file formats. showme is a viewer for meshes generated by triangle

TO RUN:

athena% add triang

athena% triangle options infile (to run triangle on input data file infile)

athena% showme options infile (to run showme on input data file infile)

There is triangle documentation, showme documentation

triangle is used by some of the demos in the IMTEK Mathematica supplement added to our Mathematica installation

See also: EasyMesh, Mathematica, tetgen

Title and Description:

ArcExplorer
Description: lightweight Java-based client for viewing GIS maps and related data

TO RUN:

athena% add arcims

athena% aejava

Documentation is here

Note:

this application was formerly in the arcej locker. It is now supplied with other administrative utilities in the arcims locker

Title and Description:

babel
Description: converts molecular description files between a variety of formats

TO RUN:

athena% babel -iinput type input file -ooutput type output file

athena% babel -H (for options and supported formats)

See also: Discovery Studio Visualizer, Jmol, Mercury, molekel, molscript, Net Entrez, rasmol, VMD

Note:

this application is no longer installed. You can install it from the openbabel Ubuntu package using aptitude or synaptic

Title and Description:

Cambridge Structural Database
Description: database of bibliographic, chemical and crystallographic information for organic molecules and metal-organic compounds. It is distributed with a number of client applications:

• Conquest (cq): search and information retrieval utility
• Mercury (mercury): structure visualization application
• Vista (vista): statistical analysis and display of geometric data
• PreQuest (prequest): database creation in CSD format
• Mogul (mogul): knowledge base for molecular geometry
• IsoStar (run_isostar): knowledge base of intermolecular interactions

TO RUN:

athena% add cambsd

athena% cq & (to run ConQuest)

athena% mercury & (to run Mercury)

athena% vista -j jobname (to run Vista)

athena% prequest (to run PreQuest)

athena% mogul (to run Mogul)

athena% run_isostar (to run IsoStar)

There are local pdf manuals, release notes, tutorials, Mercury README, pages for Mercury, Mogul, IsoStar and ConQuest; also a CSD home page and MIT Library support site

See also: Deep View, Discovery Studio Visualizer, Mercury, molscript, rasmol, Star Biochem, VMD, XCrySDen

Note:

This release will no longer run correctly on Linux Athena 9.4 machines

mercury in this locker supersedes the version in the hg locker as it is newer and integrated with the CSD; IsoStar is not fully supported at the moment and functionality related to this may be partly or completely broken

on debathena machines, you may get licensing errors unless the lines in your /etc/hosts file starting with 127.0.0.1 and 127.0.1.1 have only fully qualified host names, i.e.

127.0.1.1 zippy zippy.mit.edu

may cause denials, but

127.0.1.1 zippy.mit.edu

should be OK. You will need to be root to edit this file

Title and Description:

CPMD
Description: computational molecular chemistry application; specifically, a parallelized plane wave/pseudopotential inplementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics computations

TO RUN:

athena% add cpmd

athena% cpmd.x file.inp [pseudopotential-path] >file.out (to run commands in file.inp, generating file.out using pseudopotential in pseudopotential-path directory; if omitted, looks for pseudopotential file(s) in current directory)

There is an online manual and author site

See also: Espresso, Gaussian, molden, VMD, Xaim

Title and Description:

Deep View
Description: tool for structural analysis and display of molecular chemistry models of proteins. It can read molecular density maps and interface to a variety of tools that generate them; output in POV-Ray format is possible, allowing for the generation of ray-traced images

TO RUN:

athena% add deepview

athena% spdbv &

athena% ppov10 -w width -h height file.pov (rendered image output, file.pov made by spdbv output via File -> Save -> Pov-Ray3 Scene in ~/SPDBV/PPOV)

There is documentation and a tutorial at the author's Web site

See also: Cambridge Structural Database, Discovery Studio Visualizer, Jmol, Mercury, molden, molekel, molscript, Net Entrez, pymol, rasmol, Star Biochem, VMD, XCrySDen

Title and Description:

Discovery Studio Visualizer
Description: application that allows visualizing, analyzing and sharing biological and chemical data. Data can be viewed in multiple ways, including visually, from sequences and from data tables

TO RUN:

athena% add dsvisualizer

athena% DiscoveryStudio25 &

There is a vendor site

See also: babel, Cambridge Structural Database, Deep View, Jmol, Mercury, molekel, molscript, pymol, rasmol, Star Biochem, VMD, XCrySDen

Note:

On debathena machines there is a bug that prevents initial display of 3d molecular images; please see the bottom of the README.athena file for a workaround

Title and Description:

Espresso
Description: computational molecular chemistry applications: programs for quantum-mechanical simulations of extended or isolated systems based on density functional theory, periodic boundary conditions, plane-waves and norm-conserving or ultrasoft pseudopotentials

TO RUN:

athena% setup espresso

and in the terminal that opens:

athena% pw.x options < file.in > file.out (to run commands in file.in, generating file.out) (and similarly for other commands like ph.x etc.)

athena% pwgui & (to run pwgui interface)

There is an Espresso Web site with a User Guide

To run examples: copy subtree /mit/espresso_v4.1.1/i386_deb50/espresso-4.1.1/examples to a writable location, cd to a directory like example01 and run ./run_example

See also: CPMD, Gaussian

Title and Description:

Gaussian, Gaussview
Description: computational molecular chemistry application. Gaussian is the command-line computational engine. Gaussview is a GUI front-end to Gaussian

TO RUN:

athena% setup gaussian (for default 03-D01 version)

followed by:

athena% g03 <file.com (to run Gaussian from a command file file.com)

athena% gv & (for Gaussview interface)

See also: CPMD, Espresso, Mercury, molden, Xaim

Title and Description:

Jmol
Description: 3d molecular viewing application written in Java that can read a variety of molecular file description formats. Can be integrated as a component into other Java applications. can also export snapshot images directly, and render images using POV-Ray

TO RUN:

athena% add jmol

athena% jmol

For a sample:

athena% jmol /mit/jmol/1crn.pdb

There is an author site with demonstration pages

See also: babel, Deep View, Discovery Studio Visualizer, Mercury, molekel, molscript, pymol, rasmol, Star Biochem, VMD, XCrySDen

Title and Description:

Mercury
Description: Mercury is a 3d crystal structure visualization and exploration tool

TO RUN:

athena% add hg

athena% mercury &

There is local online documentation and a ReadMe; see also the Mercury Web page

See also: babel, Cambridge Structural Database, Deep View, Discovery Studio Visualizer, Gaussian, Jmol, molekel, molscript, platon, pymol, rasmol, Star Biochem, VMD, XCrySDen

Note:

mercury in this locker is superseded by the version in the cambsd locker as the latter is newer and integrated with the CSD

Title and Description:

molden
Description: molden is a chemistry application for displaying molecular density computed fron various ab-initio packages. It can output image description files in .pov format, suitable for input to the POV-Ray ray tracer

TO RUN:

athena% add molden

athena% molden options file

athena% gmolden options file (OpenGL-enabled version)

athena% mpfit.molden options file (mpfit-enabled version)

athena% moldenogl file.ogl (utility for displaying molden-format .ogl files)

There is an online user's Guide; see also the molden Web page

See also: CPMD, Deep View, Gaussian, molekel, platon, povray

Title and Description:

molekel
Description: Molecular graphics visualization package for displaying 3d images of molecular model and electronic structure data. Reads molecule description files in a variety of standard formats (pdb, xyz) and output data from molecular chemistry computation packages (Gaussian, adf, zindo, molden...)

TO RUN:

athena% add molekel

athena% molekel

There is 5.x online documentation, msms documentation also a Molekel home page

See also: babel, Deep View, Discovery Studio Visualizer, Jmol, Mercury, molden, molscript, pymol, rasmol, Star Biochem, VMD, XCrySDen

Title and Description:

molscript
Description: application for creating schematic or detailed molecular graphics images from molecular 3D coordinates, usually, but not exclusively, protein structures

TO RUN:

athena% add molscript

athena% molscript options -in input file -out output file

athena% molauto file.pdb | molscript -gl (to generate interactive 3d image)

To build examples:

athena% cp -r /afs/athena/software/molscript_v2.1.2/examples /var/tmp

athena% setenv LD_LIBRARY_PATH /afs/athena/software/molscript_v2.1.2/lib

athena% cd /var/tmp/examples

athena% make

There is a molscript home page

See also: babel, Cambridge Structural Database, Deep View, Discovery Studio Visualizer, Jmol, Mercury, molekel, Net Entrez, platon, pymol, rasmol, Star Biochem, VMD

Title and Description:

platon
Description: platon is a crystallographic computational chemistry tool incorporating a variety of computations and image generation formats. It can output image description files in .pov format, suitable for input to the POV-Ray ray tracer, and in rasmol format for the rasmol viewer

TO RUN:

athena% add platon

athena% platon options datafile

There is local online documentation. See also the platon Web page

See also: Mercury, molden, molscript, povray, rasmol

Title and Description:

pymol
Description: tool for displaying and manipulating 3d molecular images

TO RUN:

athena% pymol

There is online html documentation; also a Web site

See also: Deep View, Discovery Studio Visualizer, FreeWRL, geomview, Jmol, Mercury, molekel, molscript, Net Entrez, rasmol, Star Biochem, VMD, XCrySDen

Title and Description:

rasmol
Description: 3d imaging tool for displaying 3d molecular images that can be rotated in space. Reads molecule description files in standard formats such as Brookhaven Protein Databank (pdb) which is the default, as well as others (alchemy, mdl)

TO RUN:

athena% rasmol -format description_file (the launch window accepts rasmol commands after startup)

See also: babel, Cambridge Structural Database, Deep View, Discovery Studio Visualizer, FreeWRL, geomview, Jmol, Mercury, molekel, molscript, Net Entrez, pymol, Star Biochem, VMD, XCrySDen

Note:

this application is no longer installed. You can install it from the rasmol Ubuntu package using aptitude or synaptic

Title and Description:

Star Biochem
Description: Java-based 3d biomolecule viewer developed at MIT for use in courses and designed for easy, intuitive analysis commands. Accessible here through Java3D-enabled browsers

See also: Deep View, Cambridge Structural Database, Discovery Studio Visualizer, Jmol, Mercury, molekel, molscript, pymol, rasmol, VMD, XCrySDen

Title and Description:

VMD
Description: application designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies etc. It can also view more general molecules in standard representations (such as pdb and other standard molecular description files). It provides a wide variety of methods for visualizing and rendering molecules, and can also be used to animate and analyze the trajectory of molecular dynamics simulations

TO RUN:

athena% add vmd

athena% vmd

Sample data files are in the /afs/athena.mit.edu/software/vmd_v1.8.6/distrib/vmd-1.8.6/proteins directory

There is a 1.8 Quick Help page, online User's Guide and a VMD home page; 1.8.6 documentation and tutorials start here

See also: babel, Cambridge structural Database, CPMD, Deep View, Discovery Studio Visualizer, Jmol, Mercury, molekel, molscript, Net Entrez, pymol, rasmol, Star Biochem, XCrySDen

Title and Description:

Xaim
Description: computational molecular chemistry application; provides a GUI interface to programs that 1. locate critical points in the electronic charge density distribution and determine various properties at those points (extreme) and 2. plot molecular distribution functions of various quantities (molecular orbitals, electronic density, kinetic energy density...) (flopo). Can take input from the output of computation performed by Gaussian

TO RUN:

athena% add xaim

athena% Xaim &

There is local documentation and an author home page

See also: CPMD, Gaussian

Title and Description:

XCrySDen
Description: crystalline and molecular structure visualization program, which aims at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated

TO RUN:

athena% setup xcrysden

athena% xcrysden

There is local online documentation and an author home page

See also: Cambridge Structural Database, Deep View, Discovery Studio Visualizer, Jmol, Mercury, molekel, pymol, rasmol, Star Biochem, VMD

Title and Description:

XDrawChem
Description: 2d molecule drawing program similar to ChemDraw in functionality. Can input and output a variety of chemical structure formats using openbabel translator also installed in locker. Can also read structures from a database on the Internet.

TO RUN:

athena% xdrawchem

There is online documentation and an author home page

Note:

this application is no longer installed. You can install it from the xdrawchem Ubuntu package using aptitude or synaptic

Title and Description:

CHEMKIN
Description: package to investigate problems in elementary gas-phase chemical kinetics. Can be used via a GUI interface or in batch mode

TO RUN:

athena% add chemkin

athena% chemkin (to run GUI interface)

Release 4.1.1 manuals are here; also 4.1.1 help pages

to build the 3.7 version examples without running the GUI (you will need 5-6 meg. of free disk space in your home directory):

athena% add chemkin_v3.7

athena% source /mit/chemkin_v3.7/cshrc

athena% cd ~/reaction/chemkin37/samples

athena% buildsamples

See also: ePhysics

Title and description:

Electric VLSI
Description: VLSI circuit design and simulation application written in Java that incorporates many features and optional add-ons. Design features include custom IC layouts (ASICs), schematic drawing and hardware description language specifications

TO RUN:

athena% add electric

athena% electric &

There is an Electric home page, online manual, GNU Electric information page and background information

See also: dia, eagle, gEDA, gerbv, hspice, Magic, xcircuit

Title and description:

gEDA
Description: suite of electronic design tools, currently offering schematic capture and simulation tools. There are numerous tools in the suite. All can, and some must be invoked independently from the command lins. Major available components include:

• gattrib (attribute editor)
• gerbv (Gerber circuit board viewer)
• gnetlist (netlister- textual representation of a schematic)
• gnucap (GNU circuit analysis package)
• gschem (schematic editor)
• gsch2pcb (interfaces gEDA schematics to PCB layout files)
• gtkwave (digital waveform viewer)
• iverilog (Icarus Verilog compiler)
• pcb (PCB layout editor)
• vvp (Icarus Verilog simulation runtime engine)

TO RUN:

athena% gnetlist options files(s)

athena% gsch2pcb options files(s)

To run other components, consult the documentation. There is a gEDA home page and a documentation Wiki

See also: eagle, hspice, Electric VLSI, Magic

Note:

ngspice is currently unavailable; it may be accessible from the geda locker

Title and description:

GNU Linear Programming Kit
Description: set of routines packaged up into a library (libglpk.a) and a solver (glpsol) for solving linear programming (LP), mixed integer linear programming (MIP) and other related problems. The solver processes directives in a language called the "GNU MathProg modeling language" that is a subset of AMPL. The current release includes support for the GMP bignum library, which is included in the locker

TO RUN:

athena% glpsol -m sample.mod > sample.sol (to solve a MathProg model sample.mod, with results in sample.sol)

athena% gcc -o sample sample.c -lglpk -lgmp -lm (C source file sample.c, dynamic linking)

athena% gcc -o sample sample.c /mit/glpk/libglpk.a /mit/glpk/libgmp.a -lm-lz -lltdl -ldl (C source file sample.c, static linking)

For dynamic linking, you may or may not need to include the -lgmp link, depending on your code

There is a GLPK home page and a tutorial article at IBM; local docs are here (/usr/share/doc/glpk-doc on debathena machines)

See also: AMPL, ipopt, lpsolve, OPL Studio, snopt

Title and description:

ipopt
Description: application for solving general nonlinear programming problems. It is supplied as a library/API that you can link against (C/C++/FORTRAN code), and as a solver than can be invoked from within AMPL

TO RUN:

athena% add ipopt

athena% add -f gcc-4.0

athena% setenv LD_LIBRARY_PATH /mit/ipopt/lib

athena% gcc -O3 -o sample -I/mit/ipopt/include/coin sample.c -L/mit/ipopt/lib -lipopt -lm \

               -lgcc_s -lstdc++ -lgfortran -lpthread (C source file sample.c)

athena% g++ -O3 -o sample -I/mit/ipopt/include/coin sample.cpp [other.cpp] -L/mit/ipopt/lib \

               -lipopt -lm -lgcc_s -lstdc++ -lgfortran -lpthread(C++ source file(s) sample.cpp, other.cpp)

athena% gfortran -O3 -o sample -I/mit/ipopt/include/coin sample.f -L/mit/ipopt/lib -lipopt -lm \

               -lpthread (FORTRAN source file sample.f)

athena% add oplstudio (to run within AMPL)

athena% ampl

ampl: model mymodel.mod;

ampl: data mymodel.dat;

ampl: option solver ipopt;

ampl: solve;

There is an ipopt Web site, online tutorial manual

See also: AMPL, GNU Linear Programming Kit, lpsolve, OPL Studio, snopt

Title and description:

lpsolve
Description: Mixed Integer Linear Programming solver; can run via a standalone solver, a library with accompanying API which can be used to produce C, C++ and Java code and as a plugin to mathematical applications like Matlab (the latter has been installed in the matlab locker). It comes with multiple converters to convert models written in other solver's modeling languages to its native format, and can be used as a solver within AMPL

TO RUN:

athena% add lpsolve

athena% source /mit/lpsolve/set-environment

athena% lp_solve sample.lp (to use solver to solve a model sample.lp)

athena% gcc -o sample sample.c -I/mit/lpsolve/include -L/mit/lpsolve/lib -llpsolve55 -lm (C source file sample.c)

Please read this for other ways of invoking lpsolve

There is an FAQ, version 5.5 changes, online manual, Matlab guide, Java guide and API index

See also: AMPL, GNU Linear Programming Kit, ipopt, matlab, OPL Studio, snopt

Title and description:

Magic
Description: interactive editor for VLSI layouts. The IRSIM add-on is an event-driven logic level simulator for MOS circuits

TO RUN:

athena% add magic-vlsi

athena% magic options & (to launch magic)

% irsim (to start IRSIM from the Tcl prompt within Magic)

There is a Magic home page, local pdf manuals and local internal command descriptions

See also: dia, eagle, Electric VLSI, gEDA, gerbv, hspice, xcircuit

Title and description:

Meep, MPB, Harminv
Description: related utilities for analysis of time-domain signals. Meep is a finite-difference time domain signal simulator. MPB (MIT Photonic-Bands) is an application for computing definite-frequency eigenstates of Maxwell's equations in periodic dielectric structures. Harminv is a program for performing harmonic inversion of discrete-time, finite-length signals

TO RUN:

athena% add meep

athena% meep (to run Meep interactively)

athena% meep options file.ctl (to run Meep from command file file.ctl)

athena% mpb (to run MPB interactively)

athena% mpb options file.ctl (to run MPB from command file file.ctl)

athena% harminv options < input.dat (to run Harminv with input data in input.dat)

There are home pages for Meep, MPB and Harminv with further links to documentation and tutorials; also some local MPB pages

See also: matlab

Title and Description:

oof
Description: oof is designed to help materials scientists calculate macroscopic properties from images of real or simulated microstructures. ppm2oof reads images in ppm (Portable Pixel Map) format and assigns material properties to features in the image. oof conducts virtual experiments on the data structures created by ppm2oof to determine the macroscopic properties of the microstructure. Currently it calculates stresses and strains; it may also perform thermal, electric and magnetic field calculations in the future

TO RUN:

athena% add oof

athena% oof options infile (to run oof on data in infile)

athena% ppm2oof -file file.ppm (to convert file.ppm to file.goof suitable for input to oof)

Author site is here, and documentation starts here

Note:

This application is currently broken on debathena machines

Title and description:

OPL Studio
Description: modeling environment for mathematical programming and combinational optimization in the OPL modeling language

Licenses: we have 10 floating licenses

TO RUN:

athena% add oplstudio

athena% oplst & (to run release 3.7 GUI)

athena% oplrun file.mod file.dat (to run release 6.1 command-line invocation on model file.mod using data in file.dat)

There is 6.1 online pdf documentation and html documentation

See also: AMPL, GNU Linear Programming Kit, ipopt, lpsolve, snopt

Note:

OPL Studio is on Athena by courtesy of a license funded by Sloan. It is available "as is", with no end-user support. We cannot guarantee uninterrupted operation, nor that it will remain on Athena after the current license expires on 1/31/10. Questions about this can be addressed to the 3partysw@mit.edu mailing list

The GUI is only available in release 3.7. Newer releases only support command-line invocation through the oplrun command

Title and Description:

sketch
Description: software synthesis tool allowing for rapid development of tuned, bug-free algorithm implementations. The programmer develops a "sketch", or partial implementation, and a separate specification of the desired functionality. The synthesizer them completes the sketch to behave like the specification

TO RUN:

athena% setup sketch

athena% sketch options file.sk (to generate code for sketch in input script file.sk)

For samples, look in the /mit/sketch_v1.2.1/examples directory

There is documentation at the sketch Wiki site

See also: spin

Title and description:

snopt
Description: general purpose system for constrained optimization. Minimizes a linear or nonlinear function subject to bounds on the variables and sparse linear or nonlinear constraints. It is suitable for large-scale linear and quadratic programming and for linearly constrained optimization, as well as for general nonlinear problems. Supplied as a library that you can link against to generate C/C++/FORTRAN code. It can also be used within matlab and as a solver in AMPL

TO RUN:

athena% setup snopt

Please read /mit/snopt/current/README.to-run for detailed usage instructions; there is also a snopt home page

There is an online pdf manual and pointers to additional documentation in /mit/snopt/current/README.athena

See also: AMPL, GNU Linear Programming Kit, ipopt, lpsolve, matlab, OPL Studio

Title and Description:

spin
Description: spin is an on-the-fly LTL model checking system for proving properties of asynchronous software systems designs. xspin is a Tcl-based GUI front end to spin, with some added bells and whistles

TO RUN:

athena% add spin

athena% spin options data_file (for command line version)

athena% xspin & (for GUI interface version)

For tests and samples, look in the /mit/spin_v4.2.5/Test directory

There is local online documentation and more at the spin Web site

See also: sketch

Note:

spin in some modes generates C code that must be compiled into a binary that you subsequently run- generally gcc is the preferred compiler as commercial compiler preprocessors tend to have trouble with the syntax