The February issue (V80, No 2, P 277-410) of IUPAC’s Pure and Applied Chemistry Journal has a 133 pages of IUPAC recommendations for the Graphical Representation Standards for Chemical Structure Diagrams. In the Blue Obelisk context, this material is both valuable for the development of our structure representation and editing tools (JChemPaint, JCPViewer) as well as for Structure Diagram Generator (SDG) in the Chemistry Development Kit (CDK).
While the details discussed there are not particularly surprising to the educated chemist, the value of the material lies in that it is a quite complete collection of cases to take into consideration. It would be a nice document to base the next JCP-rendering-engine-related summer of code on (Not sure how far Egon and Niels got last time) and there are certainly some things which could very quickly improve the quality of output from CDK SDG, the simplest example being a horizontal alignment of the molecules longest axis.
And if you think, yes, this would be a nice project for me to help those Blue Obelisk projects, please let me know 🙂
Today was the absolute highlight in my culinary life. I had lunch at the fabulous restaurant “Schwarzwald Stube”, headed by Harald Wohlfahrt, one of Germany’s 3-Michelin-Star chefs. We went for the great 7 course menu which kept us entertained for about 4.5 hours. Following an amuse bouche, we started with tartar and mousse of mildly smoked sturgeon with imperial caviar and oyster vinaigrette. A glass of a white burgundy accompanying it was surprising in that it had the honey bouquet of a sweet desert sautern but was ultra-dry on the tongue with fruity, mineral notes.
A fried goose liver with artichokes and a caper pesto on balsamico glace formed the second course. I’m not commenting on quality – everything with no exception at all was just fabulous – fantastic material, creatively combined, cooked to the point. The service was also flawless, with a special price to be awarded to the sommelier whose recommendations where always right. The goose liver was accompanied by another white burgundy, this time with pronounced notes of oak.
The third course – scallops with a truffles from the Perigord – was especially nice because it was combined with a local specialty, Topinambur roots, their earthy, moldy 🙂 taste perfectly complementing the truffle. The main course, a potpourri of lamb with fennel compote and a mild garlic jus underpinned again Wohlfahrt’s dedication to flawless ingredients combined with uncompromising craftsmanship.
Although already slightly overwhelmed by what we had so far and time approaching 3 o’clock (we had started at noon), the cheese cart selection easily managed to revive our excitement. My memory being as bad as it is, I can only recall an ash-covered creamy goat cheese and a perfectly semi-liquid brie, but all six specimens on my cheese table where equally sensational. For both the lamb as well as the cheese we went for a Rioja, which was smooth with a well-balanced rich full body.
The first of the two concluding deserts consisted of a warm lemon biscuit on rhubarb compote, with a ginger lime sorbet served in a separate glass. The latter combination of tastes is one of my eternal favorites which I try to get where ever I can. The sommelier recommended a 1992 Riesling Beerenauslese for desert, which have lost a lot of its initial intense sweetness over the years and was now just incredible, with a wonderful acidity over fruit and honey notes.
The last course served its purpose of completely equilibrating our taste buds. A simply surprising apple-cilantro sorbet was set on a bed of mango and hibiscus juice, with a crunchy eucalyptus oblate on top.
So, it was simply astounding. We would have preferred to go there for dinner, but you need to book a dinner table up to a year in advance, depending on when you want to go (I guess, Saturday evening is the hardest). However, if you consider visiting Harald Wohlfahrt’s Schwarzwald Stube, just book a table – it will be an unforgettable event, no matter how long you wait for the evening to arrive.
A company called InfoCom, located in Arizona, advertises a product called iBioTech , which by all evidence is identical with Bioclipse. They say their iBioTech product has a plugin for chemoinformatics call “bc_cdk” (surprise :-)) and one called “bc_jmol” for 3D visualization.
While this is something that we have explicitly not tried to prevent; still it is kind of appalling to see it happen. My personal expectation on having my/our code being used by others was always that they would offer additional services and still acknowledge the original authors.
The case that we are currently seeing includes renaming and the pretension that the prodcut has been created by them (citation: iBioTech from InfoCom laboratories). The question here is of course: Is this covered by the Bioclipse license or not.
I was surprised that my first two attempts to dig into the Bioclipse license led into nowhere. There was no such thing as a LICENSE file in the top level directory in bioclipse trunk. The next thing to do was to look at the code of net.bioclipse.BioclipsePlugin.java, which in my opinion should contain a header clearly stating the license for this code. Nothing there.
But of course, the Bioclipse website has a full coverage of the license issues with Bioclipse. I would clearly say that the redistribution of a number of parts of Bioclipse, including CDK, requires the distributor to make it clear to the customer where the source code is available, which then automatically implies giving proper credit.
My feeling is that this is a case to further investigate.
At EBI, I will re-establish my research group and become leader of the chemoinformatics-related service teams, including the ChEBI and Reactome teams.
Future Directions at EBI
All of my ongoing research projects (SENECA, Bioclipse, CDK) will be continued at EBI and constitute a solid base for the rapid formation of a strong research group.
In addition, there is a plethora of fascinating modeling and data-analysis projects to be envisioned in Systems Biology in addition to the final grand goal of achieving a whole-cell or even whole-organism metabolic simulation. At EBI we will pursue the implementation of a metabolic simulation environment, with the goal of creating novel approaches to drug discovery. The “one-target, one-drug” paradigm still followed in many pharmaceutical chemoinformatics studies presented at conferences has clearly not lead to an increased number of drugs on the market and it is most importantly not capable of preventing failures of novel compounds in late clinical trials. Only a systems biology approach to drug discovery, taking into account transport phenomena, the interaction with all or as many targets as possible may allow us to make correct predictions.
To alleviate the abysmal lack of chemical data in some crucial areas of Systems Biology, we are interested in text, or better, publication mining techniques. In an ongoing collaboration with the Center for Molecular Informatics at Cambridge University, we will aim at creating an automated workflow for the extraction of molecular structures and data from the printed literature – past and present.
The Steinbeck Group offers PhD student positions via the EBI’s PhD program in 2008. Applications need to be submitted by Dec. 17 2007.
As leader of the chemoinformatics-related service teams at EBI (ChEBI, Reactome, etc.), my emphasis will be to enhance the existing resources with complete chemical semantics and raise funding for a substantial growth of the resources while securing their quality. The chemistry-related databases at EBI have the chance to become a valuable resource in pharmaceutical and medicinal chemoinformatics and serve as an integration point between chemo- and bioinformatics.
I have the pleasure to dine at the “Trüffel” (Bäckerstraße 106, D-38640 Goslar) in Goslar once every year as part of my duty to organize the German Conference on Chemoinformatics in this medival town.In 2007, I was accompanied by two of my collegues. The restaurant is usually well visited and a reservation is recommended. We all started with my favorite aperitive – a glass of Prosecco with a dash of Aperol. The started consisted of Coquille Saint-Jacques, green asparagus on a bed of basil oil. Very nice and well balanced.
The main course was a Lotte, gratinated with Mozarella, olives and other vegetables.While it was quite a tasty dish, I must say that this combination is actually a crime to the delicous texture and taste of a Lotte.I finished with a lemon sorbet with prosecco, but should have either left the prosecco away or replaced it with a bit of vodca.
We had a bottle of a delightful 2005 Gavi de Gavi, light and fruity, with all of the courses.
If you travel the Black Forrest in south-west Germany, do not forget to stop by “Die Grüne Bettlad“, owned and run by Sabin and Peter Günthner,
for a dinner.
The house was built around 1600 and has 6 rooms for those who want enjoy the excellent wines and stay for the night. Both restaurant and hotel require reservation.
Our dinner consisted of a Tafelspitz Amuse Gueulle, thena goose liver with warm brioche,followed by a ragout of crayfish and a lamb fillet with a potato gratin.
The desert was a house-made hazelnut ice with an adorable raspery gratin. There was an offer of wines by the glass, fitting each of the courses, which I gladly accepted.
The food and drinks were simply delicious, without a flaw. The only slight shadow was the bad mood of Sabine Günthner when we arrived (no causality implied :-)), but got better as the evening progressed.
This will certainly be a recurring location on our busy dining schedule.
A month ago, I stayed at the Duxford lodge near Cambridge, Uk, for a night. The room was simple but ok. The building is nicely set in park-like estate, unfortunately directly located at a busy street. When I arrived, I noticed a couple of signs saying that the restaurant had earned a number of awards and so I decided to have dinner the same evening.
At the Duxford lodge, you’ll have your aperitif at the bar and will be guided to your table just before the food is ready. This procedure seemed to be standard. If an Anglo-Saxon gourmet reads this, could he or she please enlighten me if this is that case?
Well, anyway. I asked for a Kir and got a sweet, cassis-laden warm mixture. I must say I prefer this with a very dry wine, just a dash of cassis and reasonably chilled . Enjoying the bar nevertheless – it felt like a time warp with walls covered with fighter-squadron paintings – it was just some 15 minutes before I was led into the dining room.
There, I had the chance to study in greater detail the certificates over the fire place. The restaurant has won the Rosette Award for Culinary Excellence in the every year since 2002. The award is granted by something called AA, whatever that may be (reader, please enlighten me again).
The menu started off with a pre-starter from the chef, a spicy kidney bean soup, which had an extreme
note of Cumin, nothing more than quite ok.The starter was a panfried fois-gras next to Chanterelle Boudin with Sautéd Chicory and an apple terragon emulsion. It came with a glass of a 2005 Wolf Riesling by Dr. Loosen. This was all quite delicious – my first encounter with Chanterell Boudin – and I’m still not quite sure what that is :-).
The main course, a pork tenderloin with mashed red potatoes, left mixed memories. The pork was dry, which happens
easily with lean pork but must not happen to a chef with a cullinary excellence award. The mashed red potatoes, however, were wonderful in texture and taste.I had a glass of a 2005 Conti Rossi Pinot Grigio, delightfully negligible as can be expected from a pinot grigio.
For desert, I took a Chocolate Assiette, consisting of White Chocolate Soufflé, Biscuit Pudding, Iced Layered Mousse, Mint Choc Chip Sorbet, strawberry & Milk Chocolate Tartlet – quite palatable.
A problem, as so often, was the music in the dining room – elevator style first, then pop – not quite appropriate.
Overall, I had an enjoyable dinner at the Duxford lodge restaurant.
On September 27, 2007 I had the pleasure to stay at Hotel “Felix”, Whitehouse Lane, Huntingdon Road, Cambridge, UK, for two nights.
The Felix’s location is a bit far away in the north, too far to walk if you have a heavy backpack with you. Although quite near to Huntingdon road, the heavy traffic is not recognizable. A taxi to the center was about 10 pounds, if I remember right.
The hotel’s central building is a beautiful Victorian house, spacious, with a nice mix of traditional and modern design elements in the interior. Two modern annexes have been added left and right on the rear side, forming a courtyard. I was in a room on the first floor, directly right of the elevator, which normally is a reason to ask for another room. In this case, however, the elevator was a) not used frequently and b) barely audible. The room itself was looking towards the courtyard, had a nice high ceiling, was equipped with a comfortable king size bed and a spacious bath room with a bath tub.
The “Felix” has a wireless network at a typical and therefore unacceptably high price, but I guess they can charge at these rates because everyone pays them – and so did I.
I very much enjoyed the breakfast, served á la carte in a generous living room where an open fire created a cosy atmosphere. The rest of the guests seemed to be both business men as well as academics visiting the University. Generally, the restaurant can be recommended.
Nice was the subtle understatement of the hotel, the staff was friendly, attentive and not uppish at all. I can very much recommend this place if you don’t mind being a bit farer away from the center.
The “Roka” is a wonderfully hidden place to end you day in Oia, difficult to find but only a minute away from the main marble walk way along the border of the caldera. The dishes as well as the house wine are all perfectly prepared, the service friendly and the prices extremely adequate. We tend to eat five to ten small dishes in greek restaurants – here we had not a single one which cannot be recommended and visited the place two times in this week to eat ourselves through most of the menu. The second time we went there, we met a number of people from the first visit 🙂
This was perfect. The restaurant “1800” is situated beautifully in the center of the town of Oia, right next to the small marble walk way that passes along the border of the caldera. You can either sit inside, on the roof garden (we went for this option) and in a small front court, seperated from the marble walk way by a low wall and and a cast iron fence. This latter option is very cosy, not so windy but one may (I wouldn’t) be disturbed by the constant stream of pedestrians on the other side the iron fence. The roof garden is the most popular option and worth a try. Every dish we had was perfect, as was the service. We took the full program, aperitif (a dry Martini and Kir Royal), starters, main course, a bottle of a local Santorini wine with slightly too much cask-vanilla and desert, followed by espresso and digestif, which totaled to 240 Euro. Taking into account that Oia prices are spoiled by glamor-seeking americans (this is not my interpretation but an explanation from a local whom we interviewed :-)), this was absolutely ok for the ambiente and quality of food.
I can recommend this restaurant without limitations.
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