1.2.2 ***** SeqExpress main application no longer requires server to operate Histogram visualisation now shows proportional selections Group menu code updated to order by experiment, species, platform and name Updated version and default value code New ontology loading code Ontology navigation code added Local rank and zero mean transformations added Minimal Spanning distance code added Ontology->Graph generation code added Read from local file re written Corrected upper/lower case platform id errors Pearson and manhattan distance code added Select by keyword (for local) fixed Rewrote Export as txt file code Renaming of experiments in bottom left table added Updated documentation 1.2.1 ***** Update of mixture modelling code. Now supprots number of different models (spline, line, gradient, cosine and normal) Added new clustering tool (find by slope), which is better suited to expression data than cosine/pearson Change probability model from binomial to hypergeometric ontology table viewer recalculation bug fixed cluster viewers ontology scoring bug fixed selection propagation between parallel projections fixed cosine distance measure bug fixed filter by selection fixed refactoring of hierarchical viewer (changed orientation) visualisations can now be viewed in seperate windows cluster comparison visualisation added loading of predefined categories (e.g. yeast gene regulation modules) 1.2 *** Rewrite of database side of SeqExpress (automatic maintance, schema changes) SeqExpress now only start if the database is available Added GEO integration tool updated documentation and expanded 'quick start' 1.1.8 ***** visualisation tool added for sets of clusters, used for examining 'overall trends' in sets of experiments fixed bug(s) in dendogram selection propagation/brushing removed Ontology Groups only in tools menu and replaced it with refinement menu added ontology refinement for clusters (existing groups of clusters can be examined for functional enrichment) added general (normal) refinement for clusters updated hierarchical analysis so it is able to deal with larger data sets, and included different distance measures (eucldian and cosine) report generation move to File->Export (export as html) updated documentation and expanded 'quick start' 1.1.7 ***** new grouping/tree mechanism for sets of genes auto update facility added added customisation parameters to clustering mechanisms bugs in loading data, garbage collection and threading fixed improvements to monitoring tool Report Generation tool added (outputs html description of cluster analysis etc) updated documentation (including quick start) 1.1.6 ***** co-occurance (probablistic) latent variable analysis added in Tools->Find Concepts new clustering implemented (using anchored cosine and eucledian distance EM) under Tools->Find Clusters changed organisation of Tools menu (find sub-distributions, find coexpressed, and find (kmeans) clusters renamed and moved to Tools->Find Clusters) fixed gene miss-naming bug with reloading data from .tep files updated documentation and expanded 'quick start'