EMBOSS: Project Meeting (Mon 19th March 2007)


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

1. Minutes of the last meeting

Minutes of the meeting of 5th March 2007 are here.

2. Software Development

2.1 Applications

We have been offered a fragment assembly package which we are currently evaluating as a future EMBASSY package.

2.2 Libraries

The ajStrFromFloat issue (see previous meeting) was fixed before the release.

Alan has renamed the plplot library "eplplot" to avoid clashing with later versions installed at some sites. We use a modified plplot so we maintain an older version until we can replace it.

Peter has modified "embl" format sequence output to write the new EMBL database format (from the June 2006 release). Many QA tests have changed their results and will need to be updated. Consultations are under way with the EMBL database experts on the fine detail of the new "embl" format.

Peter is documenting the details of the formats used by the ajFmt functions. David Mathog (Caltech) has pointed out that these are only documented in the ajfmt source code at present.

Peter has added a new attribute "binary:" for files and directories in ACD to mark those that contain binary data. All input files are opened "rb" (read binary) in the current code.

Alan will configure a web proxy with username and password control so that support can be added for release 5.0.0.

2.3 Web services

Mahmut has added directories (input and output) to SoapLab to support the "siggen" and "rocplot" EMBASSY applications. Input directories in SoapLab accept a list of user files. Output directories return the files written by EMBOSS to that directory.

The SoapLab server is now running Tomcat 55 with a smaller memory footprint and an easy to use server status report. The server receives a large number of requests from Taverna starting up and querying for services.

Mahmut will look into maintaining SoapLab plugin support in Taverna. The server configuration check could be made more efficient, and improvements are possible in the handling of sequence direct data (input sequence files).

2.4 Other development

3. Administration

3.1 Release 4.1.0

Release 4.1.0 is complete and successfully installed by users.

No patches have been required.

3.2 Windows release 4.1.0

Alan has released EMBOSSWIN 4.1.0.

Alan will try to build EMBOSS on Windows Vista.

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 has finished the chapter on "Your first EMBOSS application" and that is working on on "AJAX Command Definition Files".

4.2 Courses

David Judge (Univ. Cambridge) still requires the Staden spin interface for courses. At present this means using EMBOSS 2.10.0. We will try to update spin to support EMBOSS 4.1.0 when David is back from the latest course.

4.3 Website

Peter will add missing web site documentation for formatted writes and reads (see above), and will document command line qualifier naming restrictions imposed by the acdvalid utility.

5. User queries and answers

Peter and Alan have partially reviewed the lists on Sourceforge over the weekend. Many of the items are probably closed but need further checks to make sure.

Peter has a list of non-urgent new feature requests to add.

6. AOB

7. Date Of Next Meeting

The next meeting is on Monday 2nd April.