Following a recommendation by a colleague, I went to the Asia on Regent Street in Cambridge. They describe themselves as pan-Asian but I felt that there was a bit much emphasis on the indian subcontinent to be truely pan-asian.
The interior is “basic”, simplicity rules, and I had a nice table with a view on the convenience store on the opposite side of the street. I started with a glass of their favorite australian Sauvignon Blanc, the coriander crusted scallops and some prawns in oyster sauce batter. The main course was a Penang Beef with a bowl of plain rice. The sauce there was really excellent but the beef was of shoe-sole quality, really disappointing and incredibly hard to chew. The pistaccio Kulfi for desert was again very good.
While so far the service was quite good, I then did not manage to catch anyone’s attention to order a coffee for more then 15 min and then decided to leave. That kind of spoiled the otherwise quite nice experience. I’ll probably go again and give them a second chance. Overall a 4 on my scale from 0 to 10 for the food and also for the service.
Looking for a truly outstanding Japanese dining experience in a really unusual interior? The Shiro i Shiro – in waling distance to the Alexanderplatz – is it.
We asked them for selection of their choice and got:
Miso soup and silk tofu
Poached egg in a smoked broth
A selection of sushi and sashimi and kobe beef
Lamb and black cod
Udon noodles with salted butter
Accompanying the menu, we have various type of room-tempterature sakes. Everything was just perfect, including the very nice service.
SDF files are now available with ChEBI Release 56. They can be exported via the Downloads section or the search results page. We also have automatically generated links from IntEnz (www.ebi.ac.uk/intenz) and Rhea (www.ebi.ac.uk/rhea). This release contains 17842 annotated chemical entities (and not compounds Cell Phone Number Trace , as I wrote earlier – we also have classes of compounds and abstract concepts) with 74 of them new submissions entered via the ChEBI submission tool. The next ChEBI Release will be on the 27 May 2009.
all of which reported their results on the CDK wiki.
Another important outcome was a movement to join forces in creating and maintaining joint CDK-based plugins for KNIME and Bioclipse. There is a lot of synergy to be harvested. Licensing problems will need to be overcome but that seems doable. https://puttygen.in
Oliver Karch from Merck-Serono gave the last talk on Tuesday morning, showing how to visualize CDK to visualize molecular spaces in a way “as easy as Google Earth”. They us a workflow with Pipeline Pilot, a MolWind Server, which is Java and Apache based and then render 2D structures with CDK. The NASA Molwind client is then used for display. The map-like structure of the spaces visualized by projecting structures on a globe in this way depends of course on some kind of relationship leading to geographical neighborhood, such as similarity, common fragments, etc. They have come up with a sophisticated scheme of layers for visualization and providing a good zooming experience.
A nice thing about molwind is that is they have open-sourced it. It lives at molwind.org
In the second research talk on Tuesday morning Asad from EBI talks about his research on finding pathes in metabolic networks. Asad and I have been working together CUBIC in Cologne and are now again colleagues at EBI. Goal of his work has been to find patterns in biological reaction networks. His first examples deals with finding shortest pathes in a metabolic network. The problem here lies in finding maximum common substructures or calculating similarities which allow to judge which molecule in a multi-component reaction was formed out of which product. He show a number of application cases, talks about performance problems of CDK MCSS and then introduces his new tool called “Small Molecule Subgraph Detector (SMSD)”.
John has started his talk this morning by giving a manifesto for open source in drug discovery. He gives an introduction to the history of virtual drug discovery, starting in 1985 (showing some dinosaur computers :-)) and then quickly jumps to y2k. While the hardware has dramatically fallen in price, the drug discovery software still costs a hundred thousand bucks. In 2015, John envisions drug discovery to be largely outsourced and distributed in a FIPnet, a network of alliances. He also believes that the limited access licensed comp chem software will be displaced by ubiquitous open source software. He encourage us to think about what single pieces of software are actually missing to get this distributed scenario.
In a second part, he jumps to explaning a typical use case, a pharmacophore-based virtual screening setup. After a historical view back, he showed his work with Rajarhi Guha on CDKPsearch. John and Rajarshi have created an XML pharmacophore description, which allows to define a pharmacophore, walk through an SDF and find fitting compounds. John has used the package in three different application scenarios with three different companies.
To finish, John brings up the question what we would need to use a pharmacophore setup to mine the data in ChEMBL, the new Chemgenomics Resource at EBI.
Our friends from Konstanz present their KNIME workflow solution which contains the CDK for achieving cheminformatics functionality.We have a long-standing collaboration with them to help them to get CDK working in KNIME. Unfortunately, we are still at cdk 1.1 in KNIME where a number of issues prevent CDK/KNIME to perform really well.With an integration of CDK 1.2, the combination of KNIME and CDK will really rock.
For all of you out there, I’ll urge you to download KNIME from http://www.knime.org/ and try it out.
Our friend Ola Spjuth from Uppsala talks about how to access CDK from within Bioclipse using Bioclipse’s built-in scripting capabilities. Ola will cover
Bioclipse
The Use of CDK in Bioclipse
Scripting in Bioclipse
Calculating CDK properties
First we’ll download Bioclipse 2.0Beta4 from http://www.bioclipse.net.
Ola continues by explaining Bioclipse’s component architecture. For the tutorial part of his talk, he has prepared an extended set fo phantastic cheet sheats, which the user can simply run and which translate into Bioclipse scripts which are downloaded via a GIST repository. These cheat sheets can be downloaded via Bioclipse’s software update feature and I urge you to try them out.
Mark is working in my group on a CDK-based plugin for Oracle to enable chemistry searching: Similarity and Substructure. In his talk at the CDK workshop, he points out in the beginning that this is not a cartridge as defined by Oracle. It is a set of java classes loaded by the Oracle Java virtual machine (called “Aurora”).
Mark points out a few performance issues (finding all rings in a Bucky Ball :-)).
He then goes into how (and why) to use a combination of the CDK fingerprinter and the CDK subgraph ismorphism to achieve a good performance in chemical database searching. Mark has put up an exercise on http://www.ebi.ac.uk/~markr.
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The 
Oliver Karch from Merck-Serono gave the last talk on Tuesday morning, showing how to visualize CDK to visualize molecular spaces in a way “as easy as Google Earth”. They us a workflow with Pipeline Pilot, a MolWind Server, which is Java and Apache based and then render 2D structures with CDK. The NASA Molwind client is then used for display. The map-like structure of the spaces visualized by projecting structures on a globe in this way depends of course on some kind of relationship leading to geographical neighborhood, such as similarity, common fragments, etc. They have come up with a sophisticated scheme of layers for visualization and providing a good zooming experience.