barralopolis

The Gateway Arch, according to my camera.

I was too tired last night to update the blog. After another intense day of annotation, discussions, and lectures, we did the must-do touristy thing in St. Louis: visiting the Gateway Arch. It was an impressive view, and then we had some fun in the group squeezing in the small trams resembling space capsules. From the top, the view was amazing, but a bit of a letdown as the windows were so small and the glass not so clean, so the pictures did not turn out stellar. While waiting in line, I played with the stitching feature of my new Nexus 4 phone. I love my phone, and I love the camera, but trying to pan a geometrically defined and narrow structure with unsteady hands standing in line was not easy. The picture you see here is one of my attempts to capture the magnificence of the structure.

The resulting picture connects directly to the message conveyed in the second day of the workshop, still dedicated to annotation: don’t believe everything the programs tell you.

We kept working on our sandbox projects, getting them ready for submission. In the meantime, we listened to presentations by GEP students, GEP faculty, and the usual lunch lecture by Sally Elgin. Every time we have a lecture, the computers in the room become shared, stopping us from use them in the meantime. While this system probably help people to concentrate on the presentation at hand instead of working with the sequence, it does limit sharing and updating. I keep my laptop open while taking notes in Endnote, and know better than to open any page other than the GEP, Flybase, or Blast 🙂

With some practice, the mechanics of annotation become easier, and eventually it becomes almost like a game. We were warned several times to not forget or let students forget science when looking at the results. We had a good lecture explaining how Blast works, and all the possible pitfalls of believing Blast too much, as the algorithm does its miscalculations. The value of RNA ref sequences was also discussed (may be for real or may be noise, depending on the quality of work, which end of the sequence it belongs to, or simply the kind of sequence it is). We got to know another database, Blat, and we were ushered back to look really closely to the sequence and THINK about what do those sequences actually mean in the evolutionary context.

The information overload continued with Sally Elgin’s lecture about the Drosophila chromosome 4 and its unique characteristics of having 80 genes (in melanogaster) in spite of having a prominent heterochromatin nature. There was an optional activity regarding chimpanzee sequences called Chimp Chunks, but I preferred to stay in the computer lab and fight my way through another sequence with multiple isoforms. The majority of participants I talked to expressed they felt better with annotation, but they thought they would dedicate some more time to annotate in the sandbox before moving on.

Today we get started with finishing, which seems rather intimidating. I hope to update with more info and links later on, but I need to rush for morning practice now. Until next time!