EMBOSS: Project Meeting (Mon 29th September 08)


EBI: Peter Rice, Alan Bleasby, Mahmut Uludag
Apologies: Jon Ison, Shaun McGlinchey, Rodrigo Lopez, Tim Carver

1. Minutes of the last meeting

Minutes of the meeting of 15th September 2008 are here.

2. Software Development

2.1 Applications

Alan is testing and debugging the routines for index deletion code. The new code will be committed soon, when the test cycle is complete.

Peter has improved the speed (again) of the dbx indexing code. The latest change was to avoid duplicate writes from the cache by only writing a page when it is physically removed from the cache. Further complete test runs are needed to ensure correctness of the index files. Code changes will be merged with Alan's updates before being committed.

Peter will contact the submitter of 2 Perl applications to advise on conversion to C.

2.2 Libraries

2.3 SoapLab

Mahmut has completed the migration of SoapLab to new servers. The log file has only a few warnings for derived services. EMBOSS 2.8.0 is no longer being used by SoapLab. Derived services throw an error message "bad request" redirected to a message with the a recomendation ion usin gstandard SoapLab2 services. Other derived service users have agreed to move to the new services. The MIRA services will be available soon.

Mahmut will add a Perl client example to the SoapLab pages and remove redundant information on EMBOSS and SoapLab 1.0.

Mahmut will look into a PHP client for testing SoapLab services, and is looking into SPRING semantic web services with Shaun

2.4 Other

Mahmut reported that NetBeans can be used to set up an EMBOSS project easily. The EMBOSS configure script needs to be called before reading the project (a folder with lib directories, and another folder with important files such as the Makefile). The emboss.h header failed to find the include directories. it is possible to define as a source directory to fix this, but the setting is lost on restart.

3. Administration

Peter and Alan are preparing an application for renewal of EMBOSS funding, and looking at funding opportunities.

4. Documentation and Training

4.1 Books

Jon reported that the second edit of the user manual is complete. Text rearrangements will need 2-3 days. Some work still needed is marked in the section headers (autogenerating tables, for example). The developer's manual is next to be edited.

Style sheets need to be adjusted for the website.

The Appendices so far include optional sections of text (file formats etc.) and need examples to be added.

Peter has completed the code cleanup.

Content still required: For the developer's manual we need notes on usage of the libraries. The administrator's guide needs extended text on database and variable definitions.

4.2 Website

Sourceforge have removed all interactive access to their servers. We can no longer update the website from the anonymous CVS server. Access is only by sftp and rsync.

Alan has requested website space and a Wiki on the OpenBio server. We are awaiting a decision from the board of the OpenBio Foundation. Alan noted that SourceForge have changed to Apache 2.0. This broke the EMBOSS website. The .htaccess file has been updated to fix the problems.

4.3 Publications

Alan has minor revisions to the reference tables for the mEMBOSS draft.

5. User queries and answers

No new issues. Temporary solutions have been provided to some questions (removing extra text from plots).

One user asked about adding repeatmasker. We are waiting for further user responses.

6. AOB

Alan reported that Fedora updates are available again.

Mahmut had automounter problems. Opening a network attached disk as a local disk caused the automounter to loop. There is no sign of a fix in the latest Fedora updates. The application was looking for .cvs and .svn directories. It no longer looks for .trash on the network attached disks.

7. Date Of Next Meeting

The next meeting is on Monday 13th October