Last week, a sizeable flock of OPIGlets went to ISMB in Basel. Also last week, a storm and a radar tower problem over London Gatwick (LGW) and London Heathrow (LHR) led to four of those OPIGlets being stranded in Switzerland. This is a (somewhat accurate) timeline of their ordeal:
Continue readingMonthly Archives: July 2019
Trying out some code from the Eighth Joint Sheffield Conference on Chemoinformatics: finding the most common functional groups present in the DSPL library
Last month a bunch of us attended the Sheffield Chemoinformatics Conference. We heard many great presentations and there were many invitations to check out one’s GitHub page. I decided now is the perfect time to try out some code that was shown by one presenter.
Peter Ertl from Novartis presented his work on the The encyclopedia of functional groups. He presented a method that automatically detects functional groups, without the use of a pre-defined list (which is what most other methods use for detecting functional groups). His method involves recursive searching through the molecule to identify groups of atoms that meet certain criteria. He used his method to answer questions such as: how many functional groups are there and what are the most common functional groups found in common synthetic molecules versus bioactive molecules versus natural products. Since I, like many others in the group, are interested in fragment libraries (possibly due to a supervisor in common), I thought I could try it out on one of these.
Continue readingSearching through large databases with bloom filter
Searching through large databases is often a linear time problem. Here I compare the performance of applying a bloom filter and using the regular std::find command in C++:Codes are from: https://codereview.stackexchange.com/questions/179135/bloom-filter-implementation-in-c
Which fragment first?
Crystallographic fragment based lead discovery is a now a routine technique, which can sample 1000’s of compounds per week. But how do we identify the most appropriate compounds to screen against our target of interest?
Continue readingOn the Virtues of the Command Line
Wind the clock back about 50 years, and you would have found the DSKY interface—with a display (DS) and keyboard (KY)—quite familiar. It was frontend to the guidance computer used on the Apollo missions, that ultimately allowed Neil Armstrong to utter that celebrated, “One small step for [a] man, one giant leap for mankind.” The device effectively used a command line.
Continue readingFilm review: Back to the lab
Background:
Interdisciplinary projects are in fashion. Nowadays, most of the top universities in the world offer “interdisciplinary” doctorate programs. It seems that becoming a specialist in a particular field is not enough to progress in science. Now, students must prove their ability to understand and be proficient in different areas. Why study only Chemistry if you can combine it with Statistics, Programming and Biology? The more tools and concepts you can play with the better.
Continue readingJust Call Me EEGor
Recently, I was lucky enough to assist in (who am I kidding…obstruct) a sleep and anaesthesia study aimed at monitoring participants by Electroencephalogram (EEG) in various states of consciousness. The study, run by Dr Katie Warnaby of The Anaesthesia Neuroimaging Research Group at The Nuffield Department of Clinical Neuroscience, makes use of both EEG and functional Magnetic Resonance Imaging (fMRI). The research aim is to learn about the effects anaesthesia has on the brain and and in so doing help us both understand ourselves and understand how to most effectively monitor patients undergoing surgery.
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