EMBOSS: Project Meeting (Mon 2nd October 2006)
Peter is adding graph titles to "graph" plots. The "xygraphs" have a standard layout and titles defined by ACD and the command line. For the general graphs this is considerably more complicated because each plot is set up individually and there are many ways to redraw second and later plots, but does need to be made to work.
Jon is updating the HMMERNEW package top have better defaults for the number of sequences output, and a conditional prompt for the value. The hmmer user guide is referred to by the program documentation and has now been added to CVS.
Mahmut has compiled an internal 64 bit EMBOSS installation and resolved a path problem. Profiling showed SoapLab has generally very clean code with only one redundant thread for the lazy fetcher.
Mahmut is now looking at Peter Ernst's SoapLab code and using eclipse to work on typed web services.
Mahmut now has his own local EMBOSS installation for testing SoapLab. Problems with duptype autogeneration and parameter order are fixed. An XSLT issue remains.
DocBook 5 no longer has a DTD. It now uses XMLschema for validation. If we add a new schema (e.g. for ACD) we can include it within the existing namespace.
Jon will create a template for editing. The standard edition XMLmind editor is free and can be recommended for general use. The professional edition may be needed to create PDFs. Cost is about £200. Alan suggested Doxygen as an alternative.
Peter is investigating availability of XMLspy through an agreement with partners in EMBRACE.
Jon proposes a single flat directory structure to maintain the book text, expect possibly for the application documentation. Each file will have a docinfo tag with an abstract for indexing.
The book outlines are complete with titles, major sections and subsections. We need to make sure we know what parts can be completely autogenerated and estimate the number of pages for each of these. The developers book will include selected library modules.
All new issues were considered to be resolved.
Peter and Alan are away in 2 weeks time. The next meeting is on Monday 30th October.