General Issues
Software
    TOPSPIN
    MDD
    PRODECOMP
    Analysis
    AUREMOL
    ARIA
    ISD
    HADDOCK
    CING
    Deposition
    Testing

General issues

Schedule

• Empty live DVD 15 May - Dan
• Bruker pulse program map and ugraded OpenSpectra ready. 18 May - Rasmus
• USF3 format finally agreed. 18 May - Rasmus.
  

• Model change for NmrCalc interfacing, et al., ready in trunk 20 May. Tim, Rasmus.

• ISD tests finished and final 1.1/1.2 choice. 22 May - Wayne.
• Cing, ARIA upgraded to new trunk. 24 May Tim.

• Release system - software on live DVD / USB stick. 24 May - Wayne

• Working Auremol integration (very loosely coupled and somwehat peripheral) 29 May - Wayne.
  
• Functioning live DVD (software installs and works) 29 May - Wayne, Tim, All.
• Test data for testing Haddock/Aria/ISD/Cing/deposition 29 May - Wim.
  Start testing.
  
• Test data set (Histone) for processing and Analysis 29 May - Wim (or Tim?).
  
• Make sure independent working of MDD and PRODECOMP is clear, input is streamlined, and tests and data are in house. End May - Rasmus
  
• Decision on shape viewer - End May (Wayne, Tim, Rasmus).
     - Either go ahead makign new shape viewer, assignment options etc. on
       shapes
     - Or adapt to model changes temporarily, make sure usf3 input works and
       is fast, Couple more loosely to MDD/Prodecomp
  

• Analysis code freeze Mid June
  

• July 1: release (to include everything). For presentation at EuroMar meeting July 5
  

Common Software Versions

• Python: 2.5

• Numpy: 1.2.1

• Tcl/Tk: 8.5

• Data Model Current stable release.

Platforms

• Release Live DVD - Ubuntu Linux, work with any Intel chip system. 32 bit, maybe 64 bit too
• Precompiled versions for download - generic Linux, Mac(?).

Release system

To do:
Organise and set up release system

Test data

To do:
Collect and check in data.

The test system is Yeast linker Histone first domain (i.e. Hho1p GI; pdbID 1UST) (TJS). To include Projection and reduced-dimensionality experiments by Wolfgang Bermel. The data should include:

• Experimental raw data files (Bruker format)

• Processed data files (usf3 format and some standard format??

• CCPN project (in various states??)

Documentation

Status: To be done
Tutorials special for the test data are needed.
Each program to have its own documentation

License

The license agreement will likely be a sum fo the agreement for tehindivudual programs. On CCPForge Downloads will be open to registered CCPForge users. We can give people access and require accept of the license agreement first. The exact handling of licensing on the live DVD is yet to be decided.

Software

NB the details have not been updated in this section

TOPSPIN

Not part of release.

To do: Find out which version is compatible, and get hold of it for testing.

MDD

To do:
Check need for more examples
Consider further integration with Vladislav

• Code deposited. Standalone package with no GUI. 'Interface' by reading usf3 output
  Compiled executables, Csh and Gawk scripts. Documentation and examples.
  
• License: "Flexible - free for academics/education". Time-limited executables
  
• Platforms: Mac OSX, 32/64 bit Linux OK.
• Dependencies: Csh, Gawk, NmrPipe/TOPSPIN

PRODECOMP

To do:
Complete implementation of usf3 format
Shape viewer in Analysis
Integration of Shabba

• Code deposited.
  
• License: GNU GPL
  
• Platforms: 32/64 bit Linux OK. Mac OSX not tested.
  Fedora Linux OK. Redhat requires non-standard Numpy compilation for speed.
  NB must be tested for speed in pipeline environment
  
• Dependencies: Scipy 0.6.0 or higher (for Shabba only)
  

Analysis

To do:

• Code deposited.

• License: Free for non-profit use after registration. NB to be decided in detail and written.
  

• Platforms: Mac OSX, 32/64 bit Linux OK.

• Dependencies: None

AUREMOL

To do:

• Binary code only. Deposited
  

• License:

• Platforms: 

• Dependencies:

ARIA

To do:
Benjamin is working on the details. For now wait for his input.

• Code deposited. Can we expect a numpy version? If not use as is ('numeric')
  

• License: Undertaking to either make no changes or to rename files and mark changes clearly. CNS needs license.
  

• Platforms: 32/64 bit Linux OK. Mac OSX not tested.
  NB CNS must be recompiled to include ARIA specific commands.  Cns1.2 mac binaries available from Yale are not compatible with ARIA.
  

• Dependencies: CNS, Tix, Scientific Python > 2.7.2, MatPlotLib > 0.8.7 ("not fully mandatory")
  

ISD

To do:
Check bug in Pyton2.5/numpy version. Either fix or decided to use v1.1 (Tim, Wayne)

• Code: Version 1.1 (Berlin) is ready.
  

• License: "Free academic license". Register and accept disclaimer.
  

• Platforms: 32/64 bit Linux OK. Not tested on Mac.
  

• Dependencies: NB Numeric 23.8 !, CNS (to create structure from sequence file only). WHATCHECK, PROCHECK and other for report generation (optional(?))
  

HADDOCK

To do:
Resolve CNS license issue
Decide on local (with CNS) / remote (web server) distribution
If local distribution get code deposited.

• Code deposited - GUI only (?). Needs depend on whether we use local installation (no web server) local web server, or access to remote server.
  

• License:
  

  1. The program shall be used for scientific purposes only, excluding  all industrial or commercial purposes.
  2. You will provide the authors with feedback on the use of HADDOCK. Any bug reports and technical questions shall be sent to: a.m.j.j.bonvin@uu.nl
  3. The following acknowledgment shall be made in publications 
     resulting from the use of this program:
     
             C. Dominguez, R. Boelens and A.M.J.J. Bonvin (2003)
             "HADDOCK: A protein-protein docking approach based on biochemical or 
     biophysical information."
             J. Am. Chem. Soc. 125, 1731-1737.
     
             S.J. de Vries, A.D.J. van Dijk, M. Krzeminski, M. van Dijk, A. 
     Thureau, V. Hsu, T. Wassenaar and A.M.J.J. Bonvin (2007)
             "HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 
     on the CAPRI targets."
             Proteins: Struc. Funct. & Bioinformatic 69, 726-733 (2007).
  4. The program shall not be made available to users outside the 
     recipient's laboratory, unless written consent is obtained.
  5. The programs are provided 'as is' and are without warranties. The 
     authors will not be held liable for any use you make of the software.

• Platforms: Mac OSX, 32/64 bit Linux OK.

• Dependencies: CNS
  naccess for setup (not fully required - http://www.bioinf.manchester.ac.uk/nacces)
  profit (used in the analysis)  (http://www.bioinf.org.uk/software)
  Some molecular viewer (rasmol, pymol,....)
  some graph software (e.g. xmgrace)
  Local installation of web server version requires (Spider Python framework (Sjoerd de Vries, Utrecht(
  

CING

To do:
Possibly more export to CCPN project of results (Nijmegen responsibility).

• Code deposited.

• License: Standard (free for non-profit use and sign up) is OK.
  Need to arrange license/permission for DSSP.exe (Chris Sander)
  

• Platforms: Mac Leopard OK. Alan working on Linux
  

• Dependencies:
  See http://code.google.com/p/cing/source/browse/trunk/cing/Documentation/setupEclipse/development_installation_eclipse.html
  NB their fink numpy has installed: numarray-py25 1.5.2-2,  numeric-py25 24.2-3,  scipy-core-py25 1.1.1-1, scipy-py25 1:0.6.0-6, numpy-py25. Jurgen is not sure exactly what is actually used.
  

Deposition

To do:

• Deposited and working - alpha release with Analysis
  

• License:

• Platforms: 

• Dependencies:

Testing

To do:
Set up testing framework