Biowerkzeug Wiki - User contributions [en]

Hippo license

2008-10-17T21:41:03Z

Orbeckst: hippo-license.txt (from r26)

License agreement for HIPPO Beta Biowerkzeug Limited www.biowerkzeug.com

BIOWERKZEUG LIMITED IS WILLING TO LICENSE THE HIPPO SOFTWARE AND
ACCOMPANYING DOCUMENTATION (COLLECTIVELY, "SOFTWARE") UPON THE CONDITION
THAT YOU ACCEPT ALL OF THE TERMS OF THIS LICENSE AGREEMENT ("AGREEMENT").
PLEASE READ THESE TERMS CAREFULLY BEFORE INSTALLING OR USING THE
SOFTWARE. BY INSTALLING OR USING THE SOFTWARE, YOU ARE CONSENTING TO BE
BOUND BY AND ARE BECOMING A PARTY TO THIS AGREEMENT. IF YOU DO NOT AGREE
TO ALL OF THE TERMS OF THIS AGREEMENT, BIOWERKZEUG LIMITED IS UNWILLING TO
LICENSE THE SOFTWARE TO YOU ("YOU"), AND YOU SHOULD NOT INSTALL OR USE THE
SOFTWARE.

TYPES OF LICENSES

In order to install and use the Software, You must obtain one of the
following two types of licenses: (1) Non-Commercial Use License or (2)
Commercial Use License.

GRANT OF LICENSE

You may use the Software only under one of the following two types of
licenses at any time:

1. NON-COMMERCIAL USE LICENSE

Provided that you qualify for a Non-Commercial Use License as specified
above, and subject to the terms and conditions contained herein,
Biowerkzeug Limited hereby grants You, an end user, a personal, non-
transferable, non-exclusive, non- sublicensable license to install and use
the Software, free of charge, for non-commercial purposes only. You agree
that upon termination of your Non-Commercial Use License, You will cease
using the Software, destroy any copies that you have made, and remove the
Software from your computers.

2. COMMERCIAL USE LICENSE

Provided that You have selected and paid the required license fee(s) for a
Commercial Use License, and subject to the terms and conditions contained
herein, Biowerkzeug Limited hereby grants to You, an end user, a non-
transferable, non- exclusive, non-sublicensable license to install and use
the Software on the number of computers for which You have paid the
applicable fee. You agree that upon termination of your Commercial Use
License, You will cease using the Software, destroy any copies that you
have made, and remove the Software from your computers.

Biowerkzeug Limited and/or its licensors reserve all rights not expressly
granted to You herein. Any license granted by Biowerkzeug Limited under
this Agreement is not a sale of the Software or any copy of the Software.
The Software contains valuable trade secrets of Biowerkzeug Limited and its
licensors. All worldwide ownership of and all rights, titles and interests
in and to the Software, and all copies and portions of the Software,
including without limitation, all intellectual property rights therein and
thereto, are and will remain exclusively with Biowerkzeug Limited. The
Software is protected, among other ways, by the copyright laws of the
European Union and international copyright treaties. All rights not
expressly granted herein are retained by Biowerkzeug Limited and its
licensors.

USE RESTRICTIONS

You may not:

(i) use the Software, except under the terms listed above;

(ii) modify, translate, reverse engineer, decompile, disassemble or
otherwise attempt to reconstruct or discover the source code from the
binaries of the Software, except to the extent applicable laws specifically
prohibit such restriction;

(iii) create derivative works based on the Software (e.g. incorporating the
Software in a commercial product or service without a proper license);

(iv) rent, lease, sublicense, convey, distribute or otherwise transfer
rights to the Software;

(v) remove any product identification, copyright, proprietary notices or
labels from the Software.

Any and all copies made by You as permitted hereunder must contain all of
the original Software's copyright, trademark and other proprietary notices
and marks.

MAINTENANCE, SUPPORT AND UPDATES

Biowerkzeug Limited is under no obligation to maintain or support or update
the Software in any way, or to provide updates or error corrections.

CONFIDENTIALITY

The Software and any license authorization codes are confidential and
proprietary information of Biowerkzeug Limited. You agree to take adequate
steps to protect the Software and any license authorization codes, if any,
from unauthorized disclosure or use. You agree that You will not disclose
the Software, in source code or object code form, to any third party,
except as otherwise provided herein.

WARRANTY

BIOWERKZEUG LIMITED EXPRESSLY DISCLAIMS ALL WARRANTIES, WHETHER EXPRESS,
IMPLIED OR STATUTORY, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
OF MERCHANTABILITY, OF FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT OF
THIRD PARTY INTELLECTUAL PROPERTY RIGHTS, AND ANY WARRANTY THAT MAY ARISE
BY REASON OF TRADE USAGE, CUSTOM, OR COURSE OF DEALING. WITHOUT LIMITING
THE FOREGOING, YOU ACKNOWLEDGE THAT THE SOFTWARE IS PROVIDED "AS IS" AND
THAT BIOWERKZEUG LIMITED DOES NOT WARRANT THAT THE SOFTWARE WILL RUN
UNINTERRUPTED OR ERROR FREE NOR THAT THE SOFTWARE WILL OPERATE WITH
HARDWARE AND/OR SOFTWARE NOT PROVIDED BY BIOWERKZEUG LIMITED. THIS
DISCLAIMER OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF THE AGREEMENT.

LIMITED LIABILITY

THE ENTIRE RISK AS TO RESULTS AND PERFORMANCE OF THE SOFTWARE IS ASSUMED BY
YOU. UNDER NO CIRCUMSTANCES WILL BIOWERKZEUG LIMITED OR ITS LICENSORS BE
LIABLE FOR ANY SPECIAL, INDIRECT, INCIDENTAL, EXEMPLARY OR CONSEQUENTIAL
DAMAGES OF ANY KIND OR NATURE WHATSOEVER, WHETHER BASED ON CONTRACT,
WARRANTY, TORT (INCLUDING NEGLIGENCE), STRICT LIABILITY OR OTHERWISE,
ARISING OUT OF OR IN ANY WAY RELATED TO THE SOFTWARE OR THIS AGREEMENT,
EVEN IF BIOWERKZEUG LIMITED OR ITS LICENSORS HAVE BEEN ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE OR IF SUCH DAMAGE COULD HAVE BEEN REASONABLY
FORESEEN, AND NOTWITHSTANDING ANY FAILURE OF ESSENTIAL PURPOSE OF ANY
EXCLUSIVE REMEDY PROVIDED IN THIS AGREEMENT. SUCH LIMITATION ON DAMAGES
INCLUDES, BUT IS NOT LIMITED TO, DAMAGES FOR LOSS OF GOODWILL, LOST
PROFITS, LOSS OF DATA OR SOFTWARE, WORK STOPPAGE, COMPUTER FAILURE OR
MALFUNCTION OR IMPAIRMENT OF OTHER GOODS. IN NO EVENT WILL BIOWERKZEUG
LIMITED OR ITS LICENSORS BE LIABLE FOR THE COSTS OF PROCUREMENT OF
SUBSTITUTE SOFTWARE OR SERVICES. IN ADDITION, IN NO EVENT WILL THE TOTAL
LIABILITY OF BIOWERKZEUG LIMITED IN CONNECTION WITH THIS AGREEMENT OR THE
SOFTWARE EXCEED THE ACTUAL AMOUNT PAID TO BIOWERKZEUG LIMITED, IF ANY, FOR
THE SOFTWARE GIVING RISE TO THE CLAIM. YOU ACKNOWLEDGE THAT THIS SOFTWARE
IS NOT DESIGNED OR LICENSED FOR USE IN ON- LINE EQUIPMENT IN HAZARDOUS
ENVIRONMENTS SUCH AS OPERATION OF NUCLEAR FACILITIES, AIRCRAFT NAVIGATION
OR CONTROL, OR LIFE-CRITICAL APPLICATIONS. BIOWERKZEUG LIMITED EXPRESSLY
DISCLAIMS ANY LIABILITY RESULTING FROM USE OF THE SOFTWARE IN ANY SUCH ON-
LINE EQUIPMENT IN HAZARDOUS ENVIRONMENTS AND ACCEPTS NO LIABILITY IN
RESPECT OF ANY ACTIONS OR CLAIMS BASED ON THE USE OF THE SOFTWARE IN ANY
SUCH ON-LINE EQUIPMENT IN HAZARDOUS ENVIRONMENTS BY YOU. FOR PURPOSES OF
THIS PARAGRAPH, THE TERM "LIFE-CRITICAL APPLICATION" MEANS AN APPLICATION
IN WHICH THE FUNCTIONING OR MALFUNCTIONING OF THE SOFTWARE MAY RESULT
DIRECTLY OR INDIRECTLY IN PHYSICAL INJURY OR LOSS OF HUMAN LIFE.

TERMINATION

This Agreement will terminate immediately and automatically without notice
if You breach any provision in this Agreement. Upon termination You will
remove all copies of the Software or any part of the Software from any and
all computer storage devices and destroy the Software. At Biowerkzeug
Limited's request, You or your authorized signatory, will certify in
writing to Biowerkzeug Limited that all complete and partial copies of the
Software have been destroyed and that none remain in your possession or
under your control. The provisions of this Agreement, except for the
license grant and warranty, will survive termination.

MISCELLANEOUS

If any provision hereof shall be held illegal, invalid or unenforceable, in
whole or in part, such provision shall be modified to the minimum extent
necessary to make it legal, valid and enforceable, and the legality,
validity and enforceability of all other provisions of this Agreement shall
not be affected thereby. No delay or failure by either party to exercise or
enforce at any time any right or provision hereof shall be considered a
waiver thereof or of such party's right thereafter to exercise or enforce
each and every right and provision of this Agreement. This Agreement will
bind and inure to the benefit of each party's permitted successors and
assigns. You may not assign this Agreement in whole or in part, without
Biowerkzeug Limited's prior written consent. Any attempt to assign this
Agreement without such consent will be null and void. This Agreement is the
complete and exclusive statement between You and Biowerkzeug Limited
relating to the subject matter hereof and supersedes all prior oral and
written and all contemporaneous oral negotiations, commitments and
understandings of the parties, if any. In the case of any conflict between
the terms of this Agreement and the provisions of any purchase order for
the Software, the terms of this Agreement shall control.

Hippo

2008-10-17T21:38:28Z

Orbeckst: /* Download */

[[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]]
'''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ openMP]).

== Download ==
Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''.


== Installation ==
Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find
* compiled executables (see below)
** <tt>hippo</tt>: the MD and MC program
** <tt>analyse</tt>: the analysis program
* the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf])
* the [[Hippo license|license]] (to which you consent by downloading)
* the OPLS-AA forcefield file (in Hippo format)
* the readme.txt file
* the <tt>testjobs</tt> directory with example systems

The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose the following executable from the package:

{|
|+Hippo executables
!cpu !!Linux !!Windows
|-
|SSSE3 (Core Duo,...) ||<tt>hippo</tt> ||<tt>hippo.exe</tt>
|-
|SSE (PIII,P4,Athlon,...) ||<tt>hippo_p3</tt> ||<tt>hippo_p3.exe</tt>
|}

If in doubt, simply try them out in order; if it will not run you will receive an error message such as
Fatal Error: This program was not built to run on the processor in your system.
The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors
with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support.
In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum].

Executables with the <tt>_mpi</tt> extension have been compiled with OpenMP and can run on multiple CPUs. However, not all code segments are yet parallelized.

== Test cases ==
The <tt>testjobs</tt> directory contains a number of testcases.

Run the <tt>calc_testjobs_linux.bat</tt> or <tt>calc_testjobs_win32.bat</tt> script in order to perform ''all'' tests. On modern processors this should take between 2 and 4 Minutes.

Use the tests in order to get started in running your own systems.

== Features ==
=== Simulation methods ===
* [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles
* Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite>
* [[Replica exchange]] with MD and MC

=== Force fields ===
* OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite>

=== Solvation models ===
* explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>)
* Generalized Born implicit solvent (GB/SA)
* Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite>

=== Enhanced productivity ===
A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes:
* seamless restarts
* intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology
* graphical frontend under development (Windows only)

=== Analysis ===
[[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]]
A growing number of analysis tools are built into Hippo, for instance
; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state
; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure
; helicity: degree of helicity of segments along trajectory
; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite>
; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite>
; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane)
; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame.

The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used.

== References ==
<biblio>
#MMB2008 pmid=18428040
#Proteins2007 pmid=17600830
#BJ2007 pmid=17218457
#BJ2006 pmid=16339877
#JPhysChemB2006 pmid=16913813
#Proteins2005 pmid=15723347
#JACS2004 pmid=14871118
#Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d].
#Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760].
#Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985.
#Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981.
#Cordes2002 pmid=12417206
#Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>].
</biblio>

[[Category:Hippo]]
[[Category:Software]]

Gromacs

2008-06-30T21:00:31Z

Orbeckst: /* References */

'''[http://www.gromacs.org/ Gromacs]''' <cite>Berendsen1995, Lindahl2001, vanderSpoel2005, Hess2008</cite> is a MD package developed in Groningen, Netherlands, which is published under the [http://www.gnu.org/copyleft/gpl.html GNU Public license]. It's [http://www.gromacs.org/features/index.php claim to fame] is
* raw speed (due to hand coded assembly inner loops and a few optimisations)
* extensive collection of analysis tools
* coded in C

Most force fields can be used, though it only comes natively with Gromos96 (ffG43, ffG53), OPLS-AA, Encad, and the ''deprecated'' Gromacs FF ("ffgmx" – don't use it!). The Charmm FF has also been ported.

Gromacs is fairly easy to install and for Macs it is [http://pdb.finkproject.org/pdb/search.php?summary=gromacs contained] in the [http://fink.sourceforge.net/ Fink] distribution.

== Documentation ==
Gromacs comes with quite extensive [http://www.gromacs.org/content/view/13/27/ documentation] (accessible through their home page). Especially helpful are
* [http://www.gromacs.org/component/option,com_wrapper/Itemid,192/ Online Reference] manual
* [http://wiki.gromacs.org/ Gromacs Wiki]
* [http://www.gromacs.org/content/view/161/203/ Mailinglist archives]

== Tutorials ==
* [http://www.gromacs.org/content/view/137/182/ Gromacs tutorials]
* [http://www.alchemistry.org/wiki/index.php/Gromacs_Tutorials Free energy calculations] with Gromacs (from [http://www.alchemistry.org alchemistry.org])
* See also the <tt>share/tutor</tt> directory of the Gromacs distribution

== References ==
<biblio>
#Berendsen1995 H. J. C. Berendsen, D. van der Spoel, and R. van Drunen. GROMACS: A message-passing parallel molecular dynamics implementation. Comp. Phys. Comm., 91:43–56, 1995.
#Lindahl2001 Erik Lindahl, Berk Hess, and David van der Spoel. Gromacs 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod., 7(8):306–317, 2001. doi:[http://dx.doi.org/10.1007/s008940100045 10.1007/s008940100045].
#vanderSpoel2005 pmid=16211538
#Kutzner2007 pmid=17405124
#Hess2008 B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theo. Comp., 4(3):435–447, Feb 2008. doi:[http://dx.doi.org/10.1021/ct700301q 10.1021/ct700301q].
</biblio>

[[Category:Gromacs]]
[[Category:Software]]

Gromacs

2008-06-30T20:58:53Z

Orbeckst: basic Gromacs stuff + refs (uff)

'''[http://www.gromacs.org/ Gromacs]''' <cite>Berendsen1995, Lindahl2001, vanderSpoel2005, Hess2008</cite> is a MD package developed in Groningen, Netherlands, which is published under the [http://www.gnu.org/copyleft/gpl.html GNU Public license]. It's [http://www.gromacs.org/features/index.php claim to fame] is
* raw speed (due to hand coded assembly inner loops and a few optimisations)
* extensive collection of analysis tools
* coded in C

Most force fields can be used, though it only comes natively with Gromos96 (ffG43, ffG53), OPLS-AA, Encad, and the ''deprecated'' Gromacs FF ("ffgmx" – don't use it!). The Charmm FF has also been ported.

Gromacs is fairly easy to install and for Macs it is [http://pdb.finkproject.org/pdb/search.php?summary=gromacs contained] in the [http://fink.sourceforge.net/ Fink] distribution.

== Documentation ==
Gromacs comes with quite extensive [http://www.gromacs.org/content/view/13/27/ documentation] (accessible through their home page). Especially helpful are
* [http://www.gromacs.org/component/option,com_wrapper/Itemid,192/ Online Reference] manual
* [http://wiki.gromacs.org/ Gromacs Wiki]
* [http://www.gromacs.org/content/view/161/203/ Mailinglist archives]

== Tutorials ==
* [http://www.gromacs.org/content/view/137/182/ Gromacs tutorials]
* [http://www.alchemistry.org/wiki/index.php/Gromacs_Tutorials Free energy calculations] with Gromacs (from [http://www.alchemistry.org alchemistry.org])
* See also the <tt>share/tutor</tt> directory of the Gromacs distribution

== References ==
<biblio>
#Berendsen1995 H. J. C. Berendsen, D. van der Spoel, and R. van Drunen. GROMACS: A message-passing parallel molecular dynamics implementation. Comp. Phys. Comm., 91:43–56, 1995
#Lindahl2001 Erik Lindahl, Berk Hess, and David van der Spoel. Gromacs 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod., 7(8):306–317, 2001. doi:[http://dx.doi.org/10.1007/s008940100045 10.1007/s008940100045].
#vanderSpoel2005 pmid=16211538
#Kutzner2007 pmid=17405124
#Hess2008 B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theo. Comp., 4(3):435–447, Feb 2008. doi:[http://dx.doi.org/10.1021/ct700301q 10.1021/ct700301q].
</biblio>

[[Category:Gromacs]]
[[Category:Software]]

Amber

2008-06-30T20:06:51Z

Orbeckst: basic Amber stuff (mostly from Amber homepage)

'''[http://amber.scripps.edu/ Amber]''' (Assisted Model Building with Energy Refinement) refers to two things: a set of [http://amber.scripps.edu/#ff molecular mechanical force fields] for the simulation of biomolecules <cite>Ponder2003,Cheatham2001</cite> (which are in the public domain, and are used in a variety of simulation programs); and a [http://amber.scripps.edu/#code package of molecular simulation programs] <cite>Case2005</cite> which includes source code and demos. The current version of the code is Amber version 10, which is distributed by UCSF subject to a [http://amber.scripps.edu/#obtain licensing agreement].

Amber is now distributed in two parts: [http://amber.scripps.edu/#AmberTools AmberTools] and [http://amber.scripps.edu/#Amber10 Amber10]. You can use AmberTools without Amber10, but not vice versa.

== Documentation ==

== Tutorials ==
* [http://amber.scripps.edu/tutorials/ Beginners' and Advanced Tutorials]

== References ==
<biblio>
#Case2005 pmid=16200636
#Ponder2003 pmid=14631816
#Cheatham2001 pmid=11754338
</biblio>

User:Orbeckst

2008-06-30T19:47:04Z

Orbeckst: Redirecting to User:Oliver

#REDIRECT [[User:Oliver]]

Category:Python

2008-06-30T19:45:38Z

Orbeckst: New page: python is a versatile scripting language, and hence it is a preferred tool for many tasks, especially analysis of MD simulations.

[[python]] is a versatile scripting language, and hence it is a preferred tool for many tasks, especially [[analysis]] of MD simulations.

Category:Statistics

2008-06-30T19:44:46Z

Orbeckst: New page: Articles about statistical analysis.

Articles about statistical analysis.

R

2008-06-30T19:43:15Z

Orbeckst:

[http://www.r-project.org/ R] (also known as the '''R project''') is a free software environment and language for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. ''R'' is a free implementation of the statistical programming language ''S'' and ''S-Plus'' developed at Bell labs on the 80-90s. It is object oriented and provides several tools for statistical analysis, however it can be used for data manipulation, calculation and graphical display as well.

Notably, it can be used from [[python]] using '''[[rpy]]''' which makes all R functions available to python.

== Documentation ==

Essential reading

* [http://cran.r-project.org/doc/manuals/R-intro.html An introduction to R]
* [http://cran.r-project.org/doc/manuals/R-admin.html Installation and administration]

Additional reading

* [http://cran.r-project.org/manuals.html Manuals]
* [http://cran.r-project.org/faqs.html FAQ]
* [http://wiki.r-project.org/ Wiki]
* [http://www.r-project.org/doc/bib/R-books.html Books]

== Installation ==

First obtain R from one of the [http://cran.r-project.org/mirrors.html CRAN mirrors]. Or alternatively use one of the following links:

* [http://lib.stat.cmu.edu/R/CRAN/bin/windows/base/release.htm Base for wintendo]
* [http://lib.stat.cmu.edu/R/CRAN/bin/linux/ Linux]
* [http://lib.stat.cmu.edu/R/CRAN/bin/macosx/ OS-X]

Windows and Mac users most likely want the precompiled binaries listed above, not the source code. The sources have to be compiled before you can use them. If you do not know what this means, you probably do not want to do it!

* [http://lib.stat.cmu.edu/R/CRAN/src/base/R-latest.tar.gz Source code]

Then follow the instructions in:

* [http://lib.stat.cmu.edu/R/CRAN/doc/manuals/R-admin.html#Installing-R-under-Windows Windows]
* [http://lib.stat.cmu.edu/R/CRAN/doc/manuals/R-admin.html#Installing-R-under-Mac-OS-X OS-X]
* [http://lib.stat.cmu.edu/R/CRAN/doc/manuals/R-admin.html#Installing-R-under-Unix-alikes Proper *NIX]

== Using R ==

Probably the coolest ''feature'' in R is its object oriented design: almost everything is an object in ''R''. Hierarchy, operator/function overcharge and OOP in general is highly and elegantly used, thus if you are familiar with OO languages you'll have a lot of fun.

=== Package management ===

R is upgradeable via third-party packages. This packages can be updated/delete ''a la'' perl. That is, packages can be downloaded and installed from within R. First set the option CRAN to your nearest CRAN mirror using chooseCRANmirror(). Then download and install packages pkg1 and pkg2 by

> install.packages(c("pkg1", "pkg2"))

The essential dependencies of the specified packages will also be fetched. Unless the library is specified (argument lib) the first library in the library search path is used: if this is not writable, R will ask the user (in an interactive session) if the default user library should be created, and if allowed to will install the packages there.

If you want to fetch a package and all those it depends on that are not already installed, use e.g.

> install.packages("Rcmdr", dependencies = TRUE)

In case you want to compile packages yourself use

> install.packages(c("pkg1",...), type="source")

Removing packages is easy as well, from a running R process they can be removed by

> remove.packages(c("pkg1", "pkg2"),
lib = file.path("path", "to", "library"))

The command <tt>update.packages()</tt> is the simplest way to ensure that all the packages on your system are up to date.

* [http://lib.stat.cmu.edu/R/CRAN/doc/manuals/R-admin.html#Add-on-packages More information on package installation]

=== Data structures ===

There are several different structures in R namely:

'''Numbers''' : 1,2,3,5,8 ...
'''Vectors''' : myvec <- c(1,2,3)
'''Matrices''' : x <- array(1:20, dim=c(4,5)) '''or''' x <- matrix(c(1:20),4,5)
'''Lists''' : Lst <- list(name="Fred", wife="Mary", no.children=3,
child.ages=c(4,7,9))

'''Tables''' and '''Matrices''' are different structures and cannot be indistinctively used. Individual elements of an array, matrix or list can be accessed in a C-like way:
Thus for the examples above the individual elements can be accessed as:

myvec<nowiki>[[2]]</nowiki> and is the number 2
x<nowiki>[3,2]</nowiki> and is the number 7
Lst$name is the same as Lst<nowiki>[[1]]</nowiki> and is the string "Fred",
Lst$wife is the same as Lst<nowiki>[[2]]</nowiki> and is the string "Mary",
Lst$child.ages<nowiki>[1]</nowiki> is the same as Lst<nowiki>[[4]][1]</nowiki> and is the number 4.

== Reading a file ==

Say you have a file ''ufsr.plot'', which is a two column file then you might want to read it as

filename="ufsr.plot"
mytable <- read.table(filename,header=FALSE)
myvec1 <- mytable<nowiki>[[1]]</nowiki>
myvec2 <- mytable<nowiki>[[2]]</nowiki>

or alternatively

a=matrix(scan(filename,what=0),200,200,byrow=TRUE)

== Examples ==

== Emacs Speaks Statistics ==

For emacs junkies. This package provides highlighting and other cool interfaces to R (and other statistical analysis packages)

* [http://ess.r-project.org/ ESS]

[[Category:Analysis]]
[[Category:Statistics]]
[[Category:Python]]
[[Category:Software]]

Rpy

2008-06-30T19:42:43Z

Orbeckst:

[http://rpy.sourceforge.net/ rpy] is a [[python]] interface to the statistics package [[R]].

* [http://rpy.sourceforge.net/documentation.html Documentation]
* [http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/python/lin_reg/ Using Python (and R) to calculate Linear Regressions]

An example to plot a [http://www.sciencemag.org/cgi/content/full/319/5871/1772 heat map], based on a very nice [http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/python/heatmap/#Python example of how to use R from python to draw a heat map from micro array data].

<python>from rpy import r
import numpy
data = numpy.random.randn(100,30) # fake data

r.X11() # use windowing system X11
r.heatmap(a)
</python>

[[Image:Hm_gauss2.png|thumb|Example heat map from a Gaussian (mean=0, sd=1) 100x30 matrix of fake data.]]

Using an appropriate output device (pdf, png, ...) one can directly produce publication-quality images:
<python>r.library('gplots') # loads a library for heatmap.2
r.pdf('hm_gauss2.pdf') # output to file
r.heatmap_2(a,col=r.topo_colors(100),trace="none") # plot heatmap
r.dev_off() # close file output
</python>

[[Category:Analysis]]
[[Category:Statistics]]
[[Category:Python]]

Rpy

2008-06-30T19:41:32Z

Orbeckst: from Woolf Wiki

R

2008-06-30T19:40:31Z

Orbeckst: from Woolf Wiki (main author Juan R Perilla)

Visualization software

2008-06-30T19:35:19Z

Orbeckst: /* Molecules in 3D */

This page collects software that we find useful to display data from running molecular simulations. A special section is dedicated to [[#Rendering|Render]] software that create photorealistic or artistic images from scenes exported from other visualization software.

== Molecules in 3D ==
* [[VMD]]; also has extensive analysis and model building capabilities
* [[pyMol]]
* [[chimera]]
* [[yasara]]
* [[QuteMol]]
* [[pyQuteMol]]

== 1D and 2D data ==
* [[xfarbe]], a simple 2D plotter
* [[xmgrace]], for 1D plots and some graph analysis
* gnuplot
* [[matplotlib]], a python based scientific plotting library
* [[R]]

== 3D data ==
To display 3D data such as densities, you can use a typically insanely powerful 3D visualization package; see for instance this list of [http://prism.dkrz.de/Workpackages/WP4a/Low-End/Packages/WP4a_Low-End_graphic_packages.html graphics packages].
* [http://www.opendx.org/ OpenDX]: list of [http://www.opendx.org/support.html documentation] and [http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm#HDREDF native DX file format]
* viewers based on [http://www.vtk.org/ VTK] such as [http://mayavi.sourceforge.net/ MayaVi]
* [[VMD]] and [[Chimera]]

== Rendering ==
* [[Raster3D]] (the renderer can be called from [[VMD]]) and VMD's [[VMD#Tachyon|Tachyon]].
* [[Gelato]]
* [[Pixie]], a Renderman-compatible shader

[[Category:Visualization]]
[[Category:Software]]

Biowerkzeug Wiki:Site support

2008-06-30T19:33:54Z

Orbeckst: main commercial site is .com

If you are a company and you want to purchase a license for [[Hippo]] then please proceed to [http://www.biowerkzeug.com/ biowerkzeug.com].

The ''biowerkzeug community'' is free and considers your contribution to it the most valuable payment.

Thank you for visiting.

Molecular dynamics

2008-06-30T19:31:55Z

Orbeckst:

Simulating the motion of molecules by iteratively solving [[Newton's equations of motion]].

= Integrators =
* [[Verlet]]
* [[Velocity Verlet]]