Mission
The mission of the Pharma-IT Platform is the development, validation and application of novel methods and algorithms to life science data. To achieve this, the Pharma-IT Platform is integrating expertise from life sciences, provided by the Leiden / Amsterdam Center for Drug Research, as well as computer science expertise, contributed by the Leiden Institute of Advanced Computer Science and the Mathematical Institute.
News
7th Pharma-IT Interaction Meeting on 28 May 2010 (Friday)
On Friday, 28 May 2010, we cordially invite you to our 7th Pharma-IT Interaction Meeting, to be held from 4-5pm in room GORL/06 of the Gorlaeus Building of Leiden University. Details about the speakers and the program to be announced in the Pharma-IT Newsletter in due course. Hope to see you there!
Programme: "Networks and Graphs in Life Science and Pharma-IT", 4-5pm, 25 February 2010 (Thursday)
We would like to inform you of the final schedule for the 6th Pharma IT Interaction Meeting on "Networks and Graphs in Life Science and Pharma-IT" in this mail:
- Hossein Rahmani, LIACS: "Global Protein Similarity Metrics in Protein-Protein Interaction Networks"
- Michael Emmerich & Sander Hille, LIACS: "The evolution of stochastic heterogeneous networks as bet-hedging adaptations to fluctuating environments"
- Jetty Kleijn, LIACS: "Petri Nets for Bio-chemical Network Modeling"
- Eelke van der Horst, LACDR: "Graph Mining of Chemical Structures"
All talks will be short (about 10 minutes) and the goal is to identify overlap of our activities in graph-/network-related research areas.
Afterwards Michael Emmerich (LIACS) and Andreas Bender (LACDR) will present an update of the Pharma-IT Platform and we will conclude in the Leiden Faculty Club.
Day and time: Thursday, 25 February 2010, 4.00pm
Location: Gorlaeus Laboratoria (Einsteinweg 55), Room L144, Leiden University. Interested to present and network or just to listen? Feel free to join us!
Best wishes and looking forward to seeing you at the Interaction Meeting!
Andreas Bender and Michael Emmerich
6th Pharma-IT Interaction Meeting "Networks and Graphs in Life Science and Pharma-IT", 4-5pm, 25 February 2010 (Thursday)
On Thursday, 25 February 2010, we cordially invite you to our 6th Pharma-IT Interaction Meeting on
"Networks and Graphs in Life Science and Pharma-IT",
which takes place from 4-5pm in room L144 of the Gorlaeus Building (link to map) of Leiden University.
The topic of this meeting will be the use of networks (graphs) in various areas of chem- and bioinformatics, and various research groups from the LACDR, LIACS, the Metabolomics Center, the Biology Department and other institutes will briefly present their current research for networking purposes. ** You are interested in presenting as well? Please contact the organizers!** Everyone interested is very welcome to attend this meeting! Afterwards we will visit the recently opened Science Bar for further extension of the networking.
Guest Lecture of Dr Kalidas Yeturu, Indian Institute of Science, 3 July 2009
On Friday, July 3rd 2009, Dr Kalidas Yeturu from the Indian Institute of Science (IISc) in Bangalore will give a guest lecture as part of the Pharma-IT activities in Leiden. His talk will be on the "Application of Binding Site Prediction and Comparison methods in Drug Discovery - a case study with PocketDepth and PocketMatch", presenting computer algorithms to detect and compare protein binding sites. The talk will take place at 2pm in the Gorlaeus Laboratories, Room 6.
"Optimizing Drug Design": Lorentz Center Workshop in Leiden, 20 - 23 July 2009!
We are organizing the Lorentz Center Workshop "Optimizing Drug Design: Multicriteria Decision Making and Optimization in Drug Discovery and Cheminformatics" from 20 - 23 July 2009 in Leiden, The Netherlands! Travel grants for PhD students are available. For more information and registration please click here!
Spring 2009: Current Student Projects
We continuously offer student projects for master's students with a chemical/biological/life science background (e.g. from the biopharmaceutical sciences program) as well as computer scientists (e.g. with a machine learning background). Some sample current projects you could work on are listed below - if you have other scientific interests on the border between life science and computer science we are happy to accommodate them as well (please just contact us).
- Analysis of Mass Spectrometry Data for Metabolomics Compound Identification
- Barrier Trees for Analyzing High-Dimensional Data and it Applications to Drug Design
- Proteochemometrics Analysis of Ion Channel (hERG Channel) Blockers
- Two-Entropies Analysis of HIV Reverse Transcriptase Inhibitors
21 Oct 08: 3rd Pharma-IT 'Interaction Meeting'
The Meeting will take place at 12pm in Gorlaeus Lab, room L144. Miquel Rojas Cherto will talk on "Strategies in Metabolite Identification using Multi-stage Mass Spectrometry Techniques", followed by coffee and socializing. Everybody is welcome and feel free to bring your lunch!
More information to come on this site and in our current newsletter.
13 May 08: 2nd Pharma-IT 'Interaction Meeting'
The 2nd Pharma-IT 'Interaction Meeting' will bring together scientists from various universities
and pharmaceutical companies to meet and exchange ideas for future collaborations. This meeting will take
place at 2pm in room C06 of the Gorlaeus Laboratoria (map). First, Hendrik Blockeel will present his work on "Inductive Logic Programming and its applications in drug discovery", followed by coffee and discussions.
You are very welcome to sign up to our Newsletter if you wish to stay abreast with
developments in the Pharma-IT Platform and to be invited of our next meeting.
22 March 08: Publication on "Virtual Fragment Linking" Appeared in J. Med. Chem.
A publication by members of the Pharma-IT Platform entitled "Virtual Fragment Linking": An Approach To Identify Potent Binders from Low Affinity Fragment Hits was published in the Journal of Medicinal Chemistry today (DOI: 10.1021/jm701314u. In this work, which was performed at the Novartis Institutes for BioMedical Research in Cambridge/MA, we employed screening data from fragment-based screens for the prioritization of full HTS libraries. We examined conditions under which this extrapolation works in practice, and also draw conclusions for the design of FBS libraries.
28 February 08: 1st Pharma-IT 'Interaction Meeting'
The 1st Pharma-IT 'Interaction Meeting' is bringing together scientists from various universities and pharmaceutical companies to meet and exchange ideas for future collaborations. These meetings will take place periodically about 4 times a year and you are invited to sign up to our Newsletter if you wish to stay abreast with developments in the Pharma-IT Platform and to be invited of our next meeting.
5 February 08: Constitutive Meeting of the Pharma-IT Platform
Today, members of the Leiden / Amsterdam Center for Drug Research and the Leiden Institute for Advanced Computer Science convened in the Gorlaeus Laboratoria to celebrate the official start of the Pharma-IT Platform, formed by members from both institutes. The Pharma-IT Platform will be instrumental in the analysis of ever increasing amounts of data from the life sciences, being able to draw on experience from both the chemical and biological and the computer science domains. For further information about us you are cordially invited to read through the other sections of the web page.