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Asad's Blog | Man and his will to survive! | chembioinfo.com Reviews
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Man and his will to survive!
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Enzymes | Asad's Blog
https://chembioinfo.com/category/work/enzymes
Man and his will to survive! ChemBLAST: Old dog new tricks. Asymp; 6 Comments. Has a rich page dedicate to the BLAST Tool. Bringing Chemistry in the BLAST. Calculate chemical fingerprints (binary:. For a given molecule for size length L. Choose the indexes in the L which are set to. For example, if bits 1, 10, 30, …. Are set as ‘. Now transform the indexes to char terminated by ‘$’ sign ( i.e 1- B$, 10- BA$, 30- DA$ …). Concatenate the patterns to form a sequence (B$BA$DA$…). I have used ECFP4. I have ch...
Asad's Blog | Man and his will to survive! | Page 2
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Man and his will to survive! Improved Atom Typing in the Chemistry Development Kit (CDK). Asymp; Leave a comment. Atom type test cases. Improved Atom typing leads to better hydrogen handling in the CDK. Updated on : 28th July 2011. A chemically valid atom typing leads to better chemistry and consistent outputs from any chemo-informatics toolkit. In my previous post. I had highlighted the performance of the CDK atom typing on the KEGG. Group at the EMBL-EBI. We have successfully added around. From the gra...
Atom Atom Mapping (AAM) and Challenges | Asad's Blog
https://chembioinfo.com/2014/03/18/aam
Man and his will to survive! Atom Atom Mapping (AAM) and Challenges. Asymp; Leave a comment. We have just released our long awaited AAM tool in the public domain…this was long over due! You can download the tool from sourceforge. This tool is based on the algorithm published in the SA Rahman et.al. (2014) Nature Methods. Paper We have successfully mapped more than 6000 KEGG. Reactions in the EC-BLAST. The key features of this tools are:. Maps reactions catalysed by enzymes. This is build on the SMSD.
Brief CV | Asad's Blog
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Man and his will to survive! I am a Research Scientist in the Thornton group. At EMBL-EBI. My current research theme involves the investigation of small molecules and reaction mechanism. The focus of my work is to develop new algorithms and tools for understanding small molecules and their function and contribution with regards to Systems Biology. Chem-Informatics, Bioinformatics, Systems Biology, Algorithm design,. PhD (Comp. Science) at CUBIC, University of Cologne. Germany. My thesis. I Sillitoe, JM T...
CDK | Asad's Blog
https://chembioinfo.com/tag/cdk
Man and his will to survive! ChemBLAST: Old dog new tricks. Asymp; 6 Comments. Has a rich page dedicate to the BLAST Tool. Bringing Chemistry in the BLAST. Calculate chemical fingerprints (binary:. For a given molecule for size length L. Choose the indexes in the L which are set to. For example, if bits 1, 10, 30, …. Are set as ‘. Now transform the indexes to char terminated by ‘$’ sign ( i.e 1- B$, 10- BA$, 30- DA$ …). Concatenate the patterns to form a sequence (B$BA$DA$…). I have used ECFP4. I have ch...
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The plate is bad: January 2015
http://theplateisbad.blogspot.com/2015_01_01_archive.html
Thursday, January 29, 2015. Finding mass spectra with PostgreSQL: Tanimoto similarity in SQL. Now that we can store mass spectra in PostgreSQL, the next question is how to find them? There is more than one solution to this problem. One is the Tanimoto coefficient or Jaccard index. The Tanimoto coefficient T can be calculated as T = c / (a b-c). With c the number of peaks both spectra have in common and a and b the number of peaks in each spectrum. Expresses the distance between two spectra. Select (selec...
The plate is bad: November 2014
http://theplateisbad.blogspot.com/2014_11_01_archive.html
Wednesday, November 26, 2014. A working RAMDisk for PostgreSQL on Windows. Aside from the debate if this is useful or dangerous, I tried several free RAMDisks for Windows, Gavotte RamDisk, AMD Radeon RAMDisk and SoftPerfect RAM Disk - and none of them works well with PostgreSQL. Either PostgreSQL refuses to use them at all for datafiles or it seems to work, but at some point in time the server tells you, that there is something wrong. With the datafiles on the ramdrive and data corruption bites.
The plate is bad: September 2014
http://theplateisbad.blogspot.com/2014_09_01_archive.html
Wednesday, September 3, 2014. Using Code: Blocks with the Intel C/C compiler on Windows in five minutes. Code: Blocks apparently does not support the latest Intel C/C compiler out of the box. Trying to set up the necessary include paths for both the Visual Studio compiler and the Intel compiler leads to madness. But there is an easier way:. The 32 bit toolchain executables are prefixed ia32. The 64 bit ones intel64. Just start codeblocks.exe. And it works without further ado. Wednesday, September 03, 2014.
The plate is bad: Row, row, row your boat...
http://theplateisbad.blogspot.com/2015/08/row-row-row-your-boat.html
Tuesday, August 4, 2015. Row, row, row your boat. Josh Berkus gave a hint that - and how - a similar functionality might be achieved with stock PostgreSQL. Let's see, if we can analyze a continuous twitter stream too. First, we need a fast table to act as the ringbuffer:. CREATE UNLOGGED TABLE tstest.tstream. Rec timestamp with time zone NOT NULL DEFAULT clock timestamp(),. Tevent jsonb NOT NULL,. CONSTRAINT pk tstream PRIMARY KEY (rec). Written in Java using the hosebird. Tuesday, August 04, 2015. The o...
The plate is bad: February 2015
http://theplateisbad.blogspot.com/2015_02_01_archive.html
Thursday, February 26, 2015. The Long Tail - vertical table partitioning II. Having all parts from the previous post in place, some mechanism to do the routine maintenance by calling the transfer function automagically, is needed. Of course this could be done with pgAgent or it could be done with cron, but since it should be elegant, this calls for a background worker process. For illustration purposes, I wrote a sample implementation called worker ltt. To shared preload libraries. But it really works.
The plate is bad: Deriving the elemental composition from a molformula in pgchem::tigress
http://theplateisbad.blogspot.com/2015/07/deriving-elemental-composition-from.html
Thursday, July 23, 2015. Deriving the elemental composition from a molformula in pgchem: tigress. Can generate molecular formulae like C3H6NO2-. But what if we need access to the elemental composition as a relation, e.g:. Fortunately, PostgreSQL is awesome:. CREATE OR REPLACE FUNCTION elemental composition(molformula TEXT). RETURNS TABLE(element TEXT, count INTEGER) AS. DECLARE token TEXT[];. DECLARE elements TEXT[];. Elements := ARRAY['C','N','O','P','S','Cl']; - expand as needed. Count := 1;. July 24, ...
The plate is bad: August 2015
http://theplateisbad.blogspot.com/2015_08_01_archive.html
Tuesday, August 25, 2015. The 'other' cloud - parasitic storage as a service. Since some NoSQL products by default ship with no security at all, this. Was no real surprise after MongoDB. But the magnitude is astounding. How about using this for something useful? Scan the Internet for known products/servers that allow unconditional read/write access. Invent a mechanism to store data encrypted and with some redundancy, in case someone gets a wake up call. Build a service around 1, 2, 3, and 4. And now, som...
The plate is bad: October 2014
http://theplateisbad.blogspot.com/2014_10_01_archive.html
Thursday, October 30, 2014. ToroDB Adventures: Adding unimplemented commands. Ok" : 0, "errmsg" : "Unimplemented command: create", "code" : 1000002 }. Ok" : 1 }. In five simple steps:. 1) Find out how the command is called internally. toroDB tells you that in the message:. So it is "create". 2) Look up the "create" command. Start in QueryCommandProcessor.java. 3) "create" does nothing at the moment, so add some code. I just copied it from "createIndexes" so. 4) Now, ProcessorCaller. Class, make it known.
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Chemistry & Biodiversity
Serves as a high-quality. Publishing forum covering a wide range of biorelevant topics for a truly international audience. Chemistry and Biodiversity. Publishes both field-specific and interdisciplinary contributions on all aspects of biologically relevant. Wiley-VHCA AG (former Verlag Helvetica Chimica Acta). 41 44 360 24 34. 41 44 360 24 35. Send mail to webmaster@chembiodiv.ch. With questions or comments about this web site.
Chemistry & Biodiversity
Serves as a high-quality. Publishing forum covering a wide range of biorelevant topics for a truly international audience. Chemistry and Biodiversity. Publishes both field-specific and interdisciplinary contributions on all aspects of biologically relevant. Wiley-VHCA AG (former Verlag Helvetica Chimica Acta). 41 44 360 24 34. 41 44 360 24 35. Send mail to webmaster@chembiodiv.ch. With questions or comments about this web site.
ChemBio Quest.
You can now move on to level 2 by clicking the "NEXT" button above. Ok, ready to go into the cave and give it a shot for real? This field is optional, but required for TriC students who wish to record their results. The Idol Code allows you to skip to level 2 and play with infinite mode on. The game will not end and you will never run out of lives. You can enter an email address to send your results to.
Enable Entrepeneurial Research and Discovery ®
Research Informatics for Groups (Labs). Ontological separation and isolation of scientific pursuit precipitates naturally within organizations (already) at the lab or group level. Nouns and verbs that characterize things and activities vary wildly across the landscape. A data management solution in this arena must mold and shape itself toward the will (and intention) of the scientists engaged in doing the daily work of research and discovery. Entity / target registration (compound or organism). The usage...
Asad's Blog | Man and his will to survive!
Man and his will to survive! A Romance between Biology and Chemistry – Protein Sequences, Molecules and Enzyme function! Asymp; 3 Comments. NGS) data is knocking at our door and simultaneously, our ability to design novel enzymes. Rational design or directed evolution) using high throughput methods has improved tremendously. As a result, the demand to link enzymatic sequences to their chemical products and metabolic pathways is ever increasing. On the other hand, the push to generate Metabolomics. Predic...
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Future home of something quite cool. If you're the site owner. To launch this site. If you are a visitor. Please check back soon.
ChemBio Journal
Tuesday, August 4, 2009. Atoms and molecules are the building blocks of matter and therefore everything has molecules in them. However I still think that using the books and their information are still more reliable , trustworthy and also easier to use. This may be because that these books are published and are commented by different people and publishers. Overall I feel that this chemistry journal has been a great help to me. Posted by Aaron Lau. Sunday, July 26, 2009. A soft reactive metal. Today I wil...
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