EMBOSS: Project Meeting (Mon 2nd April 2007)


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

1. Minutes of the last meeting

Minutes of the meeting of 19th March 2007 are here.

2. Software Development

2.1 Applications

Peter has added an option to infoseq to display the database name.

Alan reports a problem with file pointers in edialign under Windows. He has a temporary fix and is investigating further.

2.2 plplot Library

Peter has been converting PLPLOT 5.7.2 (release 5.7.3 appeared immediately afterwards) so that we can use the latest plplot code instead of the older release included in EMBOSS 1.0.0. The primary motivation was to fix the long-standing problem of requiring PseudoColour mode when launching EMBOSS graphics through X11 servers on Windows. This is fixed in later releases of plplot.

The current EMBOSS code has a kludge for PNG image sizes. The new code will replace this with a direct call to the plplot image size function. This applies to all graphics devices for now, but we can intercept the call in AJAX ajgraph.c and limit it to image files if appropriate.

The code generated a large number of compiler warnings. If we continue to use the latest plplot code we should try to fix these in plplot itself. Most were missing "const" attributes for strings.

Alan is looking into building the EMBOSS new plplot library code on Windows where Andre Blavier's EMBOSSWIN port used a Makefile to build a static library from native plplot code and ignored the code in EMBOSS.

One side effect is that the latest plplot requires a more recent release of the gd library to support anti-aliasing, and this includes revived support for GIF graphics.

Nothing will be committed until all issues are resolved.

2.2 Other Libraries

Peter has extended support for reading EMBL sequence format to preserve all fields. When written in Genbank format almost all fields in GenBank are reported - except for the GI number which is not included in the EMBL entry. A sequence version number is required in EMBL and Genbank formats. After discussion with EBI external services, we will use "1" if no other version is known. Zero is already allocated to deleted entries.

2.3 Web services

Mahmut has an SVG renderer for EMBRACE workflow output. He will try adding it to Taverna as a plugin.

The SoapLab EMBOSS 4 server was restarted to fix an httpd crash.

Martin has rejoined us as a visiting scientist. Early efforts will be to complete SoapLab 2.0. The acd2xml java utility may require some XML changes. This parser is based on a yacc grammar. Peter offered to investigate possibilities to generate the grammar automatically to keep up with ACD syntax changes. There are plans to provide a GUI for service providers before the final release.

SoapLab now has a plugin mechanism for grid services, which will make features such as exception handling easier to implement.

Martin is working on GowLab interfaces to EBI web services.

2.4 Other development

3. Administration

3.1 Release 4.1.0

Peter has released the first patch to fix issues in graphics output for banana and prettyplot.

3.2 Windows release 4.1.0

Alan reports success in building EMBOSS on Windows Vista.

Alan is looking into compilation of the plplot library code on Windows.

3.3 Other operating systems

The IBM loan machine goes back today (the loan period has ended). No news yet on a possible replacement.

Alan may install AFS to test EMBOSS and Jemboss.

4. Documentation and Training

4.1 Books

Jon is working on on "AJAX Command Definition Files" syntax and guide for authors. He has some updates to the documentation in the tables which need to be copied into the main code (as the tables are generated automatically).

5. User queries and answers

No new issues.

6. AOB


7. Date Of Next Meeting

The next meeting is on Monday 16th April.