• Methoximation results in a syn- and anti- isomer
  • Gehirnsand findet sich in der Zirbeldüse, die u.a. auch Melatonin und Epithalamin produziert
  • Cats use a 21st amino acid called taurine.
  • Partial Least Squares Discriminant Analysis (PLS-DA) is a supervised learning pattern recognition method, try HOLMES.
  • PUBCHEM is a freely accessible database created by NIH in 2004 to provide information about small organic molecules.
  • Seniors theorem on molecular graphs was published in American Journal of Mathematics, Vol. 73, No. 3. (Jul., 1951), pp. 663-689.
  • Gegacker eines elektronischen Huhns findet sich auf Maschinenwelt.
  • Fiehnlab@Web Fiehnlab RSS Feed gibt Auskunft ueber das Verhalten des "Fiehnlabs" im Internet.
  • Honest trees are trees which are not only understandable and accurate, but also statistically reliable.
    To be honest, there are also Classification Trees, Regression Trees and Boosting Trees and Adaptive Trees - see here.
  • Sumanirole [179386-43-7] is a parkinson (pipeline) drug
  • Bananas have not had sex for 10,000 years. Edible bananas are mutants with three sets of chromosomes (triploid), instead of the two found in wild bananas. Keyword: seedless bananas (kernlose Bananen),
  • Parasitic computing for QSAR purposes can be performed at the VCCLab - provided by Igor Tetko. As this services serve the scientific community one can call them rather symbiotic computing :-)
  • Candidatus Brocadia anammoxidans belongs to anammox bacteria, using anaerobic ammonia oxidation.
  • Cangrelor [163706-06-7] C17H25Cl2F3N5O12P3S2 is a platelet P2T receptor antagonist and platelet aggregation inhibitor in Phase I
  • "Thermo Finnigan LXQ" is a new new cost-effective linear ion trap mass spectrometer, thus a 2D-quadrupole field ion trap with higher sensitivity than a normal 3D ion trap.
  • Text Mining inlcudes Latent Semantic Indexing and Feature Selection and can be used for Emerging Trend Detection.
  • CRC-Press offers books on view-before-buy basis for Engineering, Neurosciences, Infosecurity, Statistics, Math, Environment, Forensic, Food Sciences.
  • Image Processing for automated cell counting in life sciences (or coin counting)
  • How bad software producers get kicked out: The free lunch is over (bad - means software is not multithreaded)
  • mzXML and netCDF and Thermo raw file converters.
  • Theoretical Plates: A one meter monolithic LC column can have a plate number of 80,000 theoretical plates (Merck Chromolith, linked columns). The UPLC can reach plate numbers of 100,000 theoretical plates with a 45 cm setup of linked columns (Waters UPLC) and a typical GC column of 30 m length and 0.25 mm internal diameter usually reaches a column efficiency of 125.000 theoretical plates.
  • The painful evolution of combinatorial chemistry, some of the players and counter-players and some documents about split-synthesis and the cornucopia of peptides.
  • If you have crows around your house and they are too loud play the owl, the hawk and bald.
  • IBM Almaden Chemical Search alpha allows searching chemical structures in patents which is usually a domain of CAS Scifinder and Derwent. Patent search includes Markush structures but also can be done with a name to structure conversion (see ChemAxon Marvin or Oscar3). Check out the publication MINING PATENTS USING MOLECULAR SIMILARITY SEARCH it includes a very pretty and sophisticated method using InChI and textmining.
  • Thesis by Yongquan Han Evolutionary Algorithm as an Approach for Computer Assisted Structure Elucidation of Organic and Bioorganic Compounds
  • SIMCOMP - was used for running an MCS on KEGG
  • iAF1260 - (metabolic network reconstruction) contains a comprehensive picture of E. coli metabolism [PMC1911197].
    "iAF1260 represents the largest metabolic reconstruction of any unicellular organism and accounts for 1260 open reading frames ORFs(28%) in the current E. coli genome" and "1161 ORFs included in iAF1260 have been experimentally verified." [DOI] - See supplement data in XLS and MOL format. See also [Cobra Tollbox]
  • MS profiling data from various (latest) metabolic profiling platforms can be found at the NSF 2010 website. This
    includes data from GC-MS, LC-MS and infusion MS covering a large range of primary and secondary metabolites. The sets are very useful for comparison of the different metabolomics platforms. Also it shows the lack of unique identifiers.
  • Acovea 5.0 is a program for optimizing GCC (or C++) GNU C Compiler options via genetic programming. Such an approach is in general adorable because most of the unexpected combinations can be tested to increase performance of C or C++ programs. Howver certain Compilers like Intels aggressive optimizing compiler can still be faster than gnu CC. Also Microsoft usually is an early adopter of streaming commands for new AMD and INTEL CPUs (including SSE, SSE2,SSE3,SSE4, AMD64).
  • CUDA is a computer language and compiler using streaming extensions on GPUs (graphic cards). In single precision (FP) mode up to TFLOP/s are possible in double precision mode still 500 GFLOPs. The compareable AMD/ATI approach is not successful enough with graphic cards of the same quality (mainly because of lacking compiler support and knowledge). With the NVIDA CUDA TESLA cards or cluster components TFLOP speed is available to average consumers for the first time. The problem here is that streaming compilers require a totally different programming approach, which is unfortunately not thought at many universities.
  • UC Davis CHNR - the Center for Health and Nutrition Research was built with a donation from BASF Corp., Daiichi Pharmaceutical Co., Ltd., Eisai Co., Ltd., Aventis Animal Nutrition S.A. Rhone-Poulenc Animal Nutrition, Hoffman-La Roche, Inc., Roche Vitamins, Inc., per court order VITAMIN CASES, 301803
  • Maillard and lipid oxidation products from the EU HeatTox project. This contains a Maillard database lists with approximately 570 volatile compounds, while approximately 200 volatile compounds are listed as products of heated lipid systems. Those products occur in well curated Bemmchen or fresh bread with a nice thick brown good smelling yummy crust. Guten Appetit!
  • MSTFA (CAS: 24589-78-4) and Methoxylamine hydrochloride (CAS: 593-56-6) are used for derivatization in GC-MS. The quality must be monitored for every single batch prior use. Although several companies provide high quality solvents (p.a. or pro-analysi) they seldom perform a complete GC-MS analysis in the low boiling (volatile) and high-boiling range for each batch. NMR analysis and boiling point or refraction analysis are not sensitive enough to detect contaminations. Interferences in the low boiling range come from impure solvents and chemicals during synthesis and dirt peaks in the high boiling range from oil or fat contaminations used on glassware. That is also the reason why solvent blanks and method blanks and quality checks must be performed before every metabolic profiling experiment. Furthermore request a GC-MS purity analysis for each batch with the Certificate of Analysis. See commercial sources for MSTFA.xls and Methoxylamine-hydrochloride.xls
  • www.5iantlavalamp.com is a domain from microsoft.com which transfers to MS Office products. It is found by opening documents with TextPad or by virus scanners. For example: urn:schemas-microsoft-com:office:smarttags http://www.5iantlavalamp.com/Z or http://www.5iantlavalamp.com/B
  • AntRenamer is a neat tool to batch rename multipe files. Sometimes hundreds of files need to be renamed. This is not a problem for programmers who know DOS, Perl, Powershell. However the GUI based AntRenamer can do it very fast. It can rename numbers, multiple string replacements, enumerations, random names, regular expressions and even has a preview function.
  • Ohhhh the sugars including but not limited to Cellobiose, Erlose, Fructose, Gentiobiose, Glucose, Isomaltose, Kestose, Kojibiose, Laminaribiose, Maltose, Maltotriose, Maltulose, Melezitose, Melibiose, Melibiulose, Neohesperidoside, Nigerose, Palatinose, Panose, Raffinose, Rutinose. Sophorose, Sucrose, Trehalose, Turanose. Get some books here [PDF] [PDF]
  • BatchEntrez is the PubChem Service to retrieve list of PubChem CIDs or batch CIDs (compounds and substances) from PubChem. It is a hidden link and can be used if no PUG PowerUserGateway or ENTREZ/SOAP programmer is available and PubChemSR cant be used. So just put a list of compound IDs into a text file and submit to BatchEntrez. See also the PUG SOAP examples for Taverna, Pipeline Pilot, Java (with Axis), Java (with Axis2), Python (with ZSI), C# .NET 2.0 (Visual Studio 2005), Visual Basic .NET 2.0 (Visual Studio 2005), Perl (SOAP::Lite).
  • JCAMP2Matrix can be used to convert mass spectra into an XY matrix. The tool requires data from Lib2NIST.
  • Compound Annotation for the paper: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression [DOI] and the overlap between our chemicals list, annotated with InChIKeys..
  • An electron impact (EI) spectrum of benzene from 1932 is shown in: Mass-Spectrograph Study of the Ionization and Dissociation by Electron Impact of Benzene and Carbon Bisulfide; Phys. Rev. 41, 149 - 153 (1932); Ernest G. Linder; [LINK]
  • Are you tired today in Davis, CA, 65616 and 95618? Many people complain they are tired from work, they are near Karoshi (japanese: death from overwork), have terrible headaches etc. pp., nevertheless they simply forgot their double shot of Espresso quadrupled and they did not check the local air pressure. Check the barometric pressure (graphics below) don't forget to look at the weather WunderMap - a mashup of satellite, weather and webcam data [WunderMap LINK]:
  • NestedVM can be used to convert C or C++ code into JAVA using a bytecode compiler. Therefore any application written in C or C++ can be run in JAVA (via MIPS code). Examples see Depth-First.
  • WALTER JENNINGS: An Honorary Colloquium with interesting slides aromas, VOCs, prepGC, NMR, purge/trap
  • Qtap-QqTOF-MS would allow MS/MS of complete scan range, no data-dependent scans required; RP=200 @ 1000 Da in Qtap; tapered rod geometry [DOI]
  • Types of ion traps: "cylindrical ion trap", "linear ion trap", "rectilinear ion trap", "toroidal ion trap", "Halo ion trap
  • When opening netCDF (*.cdf) files using AMDIS, a popup may pop up, saying: Fast User Switching must be disabled. You have to be an Administrator to do that. Solution: Rename Varian DLL's Wscomm32.dll to *.dll- (see the "-" at the end. Like: Wscomm32.dll just rename them to Wscomm32.dll-
    Problem solved! Of course in order to read Varian files you need to rename the file back to original.
  • A glass of milk may prevent a severe outbreak of Escherichia coli O157:H7 (Shiga toxin). E. coli O157:H7 (EHEC) and their related bacterial proteins or Shiga toxins utilize gangliosides GT1, GD1b, GM1 and GM2 as receptors on host cells. And another publication that says otherwise "Glycosphingolipids are not pivotal receptors for Subtilase cytotoxin in vivo: Sensitivity analysis with glycosylation-defective mutant mice" (doi:10.1016/j.bbrc.2008.10.163).

    Anti-infective agents containing gangliosides against Escherichia coli O157:H7. Sato, Norifumi. (Snow Brand Milk Products Co., Ltd., Japan). Jpn. Kokai Tokkyo Koho (2001), 5 pp. CODEN: JKXXAF JP 2001002704 A 20010109 Patent written in Japanese. Application: JP 1999-172634 19990618. Priority: JP 1999-172634 19990618. CAN 134:66131 AN 2001:17861 Patent Family Information: Patent No. Kind Date Application No. Date
    JP 2001002704 A 20010109 JP 1999-172634 19990618, JP 3521067 B2 20040419, Priority Application
    JP 1999-172634 19990618

    Abstract (CAPLUS)
    The anti-infective agents, useful for preventing infection by E. coli O157:H7 and worsening of symptoms due to verotoxins such as hemorrhagic colitis and hemolytic uremic syndrome. Germ-free mice were orally given milk-derived ganglioside GD3 and inoculated with enterohemorrhagic E. coli O157:H7 on the 3rd day from the start of the ganglioside administration. Survival rate after 8 days was 65%, vs. 35% for an untreated control group. Extn. of gangliosides from butter milk or a whey protein conc. and manuf. of a nutrient compn. contg. the ext. and tablets were also shown.

  • A petabyte on a budget - 90 TByte for 5617 Dollars (with Samsung F4 F4EG 2 TB hard drives), so 11 systems would be 62k
  • Windows7 64 bit with INTEL AHCI Matrix RAID and AHCI SAS drivers, FUBAR Error: "Windows is unable to install to the selected location. Error: 0x80300001" Solution: insert Windows DVD. Explanation, after installation of SAS and RAID drivers from a second location, such as INTEL SCU C600 CHIPSET SAS RAID or C600 CHIPSET SATA/AHCI the RAID drives are recognized and drivers are laded from the secondary DVD, but for further installation the Windows DVD has to be inserted. Error should be correctly named: "Please insert WINDOWS DVD" because the reference to an existing partition is confusing.

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