Page ThesisAnnoAlignReports

Week 0 (21.10.2009 - 25.10.2009)

• First meeting with David and Marcel
• Recieved topic and short introduction into the topic
• Recieved first supplemental material (3 Papers)

Week 1 (26.10.2009 - 01.11.2009)

• Started working through the material to familiarize myself with the topic

Week 2 (01.11.2009 - 08.11.2009)

• Read documentation on the FragmentStore
• First experimental testing code on FragmentStore usage

Week 3 (08.11.2009 - 15.11.2009)

• Wrote summary for the wiki
• Started theoretical work on the pipeline

Week 3 & 4 (15.11.2009 - 30.11.2009)

• Downloaded and processed testing data (files are not checked into the svn due to file size restrictions and common sense)
• Got a Perl script from Marcel that transforms gtf into gff and deletes unneeded records
• Wrote code that reads the data into the fragment store and connects each annotation with the corresponding contig (depending on the begin- and endposition)
• Open Questions: How to load the read data dynamically as needed?
• Perspective: Write a datastructure that aggregates all annotations & the sequence belonging to one "gene" and build a function that creates the splicing products using this datastructure

Week 5 (01.12.2009 - 07.12.2009)

• Was really sick, had to stay one day in hospital, therefore couldn't continue work

Weeks 6 - 11 (07.12-2009 - 10.01.2010)

• wrote more code to read the data into the according stores (Annotations, AnnotationNames, Contigs)
• implemented a new datastructure to gather all annotations belonging to one parent (= a transcript)
• investigated an alleged bug in the GTF parser with marcel
• Christmas & New Years Eve

Week 12 (11.01.2010 - 18.01.2010)

• Meeting with David to work on the above mentioned bug (which was not really a bug rather than a misinterpreted behavior) and to discuss the next steps in the project

Week 13 (18.01.2010 - 25.01.2010)

• implemented several sorting steps to ensure that transcript objects are in order in preparation for the splicing proxy construction
• prepared a LaTeX structure for the thesis paper