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About the classic papers club
The aim of this club is to read the papers that everyone keeps citing but which few people have read. We plan to read a paper every third week for the next 20 years.
We tend to meet Wednesday mornings, and tend to announce the papers we will read ahead of time. Everyone is welcome: if a paper sounds interesting to you, please come by.
This reading group used to be organised on facebook. The old page can be found here.
About the Science Book Club
- Mathematical Chemistry and Chemoinformatics, by A. Kerber et al. (summary part I and part II)
- Phylogeny: Discrete and random processes in evolution, by M. Steel (review published on SIAM News Blog: part I, part II, part III)
- Bayesian Methods in Structural Bioinformatics, edited by
T. Hamelryck, K. Mardia and J. Ferkinghoff-Borg
-
Phylogenetics, by C. Semple and M. A. Steel
- Protein Physics – A course of lectures, by A. V. Finkelstein and O. Ptitsyn (summary slides)
About the Humanities Book Club
This book club is an endeavour to broaden our horizons and critically engage with good writing from across the humanities. We intend to go through a book per term, and tend to meet roughly once every 3rd week to discuss new sections of whatever book we are currently going through. Past books that we have read include:
- The General Theory of Employment, Interest and Money, by John Maynard Keynes
- The Qurʼān – A New Annoteted Translation, by Arthur J. Droge
- On Politics, by Alan Ryan
- Capital in the Twenty-First Century, by Thomas Piketty
The size of the reading group is capped at 6 persons. Current members include Jotun Hein, Mathias Cronjäger, James Anderson (former DPhil student), and Eddie Rolls (former summer school student).
Graph Grammar Library
Summary of the paper “The Graph Grammar Library – a generic framework for chemical graph rewrite systems” by Flamm et al.
The paper explains how a C++ package works, which implements graph grammar rewriting rules for chemical reaction networks. There are some other chem(o)informatics stuff in the package as well.
The main story of the paper is that Yadav et al. requested a package like GGL, which is now available.
Most of it seems quite logical/intuitive based on the what it tries to do.
The software translates to/from SMILES at the beginning and end, but everything is done using graphs.
For more information and guides on how to use the software, see: http://www.tbi.univie.ac.at/software/GGL/
Mathematical Chemistry and ChemoInformatics part II
Jotun Hein and William Kurdahl will review two books: Leach and Gillet (2010) Introduction to Chemoinformatics and chapters from Faulon Handbook of Chemoinformatics Algorithms (2007). Additionally briefly summarize key papers on Graph Grammars, Reaction prediction and related topics. The talk ends with an attempt to identify projects in chemoinformatics that would be worth it to work on.
The slides can be found here: http://tinyurl.com/j28y67s
Thursday December 8th 10AM to noon LG Department of Statistics
HEIN RESEARCH 