EMBOSS: Project Meeting (Mon 18th August 08)
Peter is checking the modifications made to the profiled code to make sure that all results match the current release.
Peter has reviewed the data files used by dan to improve documentation and to standardise the free energy values to 25C. The free energy values are ignored by all code at present and are recalculated for a specific temperature.
Modifications to enable LSF support were not trivial as the SoapLab service description refers to a Java classname. Martin has been contacted for advice.
The ExecuteThread class executes jobs, used standard input and records standard output and standard error. The basic iomplementation has been tested apart from temporary input files (e.g. for mwcontam) as this needs a tmp directory visibvle on both systems. Tests used EMBOSS5. External services have now installed EMBOSS 6.0.1.
Legacy derived services support should be dropped. The inputs need a web servcie call for each attribute. Only a few clients have used these services. Mahmut will try to contact the users.
Alan has added patches and updated mEMBOSS. These include multiple sequence support in jaspscan, a fix to digest and a fix for PCRE missed matches in fuzznuc
Jon is marking up the text of Lisa's chapter updates.
Jon has drafts of EMBOSS papers, using text from the manuals.