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Chem-bla-ics
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- January 22, 2013
- 04:09 AM
- 194 views
ToxBank: the next generation toxicology
by egonw in Chem-bla-ics
Before I moved to my current position in Maastricht, I had the great pleasure to work with Prof. Roland Grafström (check his pathway bioinformatics done with his then PhD Rebecca) and Prof. Bengt Fadeel at the Karolinska Institutet. During this year I part-time worked on ToxBank and part-time on nano-QSAR, and worked on semantics, predictive toxicology, and Open Data. This blog post is about the ToxBank work.
I promised firework, and the first rockets are heading upw........ Read more »
Kohonen, P., Benfenati, E., Bower, D., Ceder, R., Crump, M., Cross, K., Grafström, R., Healy, L., Helma, C., Jeliazkova, N.... (2013) The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing. Molecular Informatics. DOI: 10.1002/minf.201200114
- November 18, 2012
- 03:39 PM
- 229 views
DHSs and histone modifications: methylation, acetylation, citrullination, and phosphorylation
by egonw in Chem-bla-ics
One day on, and still struggling with the chemistry behind gene regulation. Let no biologist ever tell me again not to use acronyms (yes, I am looking at you!). But it is interesting. I learned a lot about ChIP, histone modifications, etc, etc. This is an amazing world, where specific histone complex protein residues get methylated, acetylated, citrullinated, and phosphorylated. Of course, all this is in the context of the ENCODE meeting we have tomorrow at BiGCaT, where I will try to ........ Read more »
Thurman, R., Rynes, E., Humbert, R., Vierstra, J., Maurano, M., Haugen, E., Sheffield, N., Stergachis, A., Wang, H., Vernot, B.... (2012) The accessible chromatin landscape of the human genome. Nature, 489(7414), 75-82. DOI: 10.1038/nature11232
Felsenfeld G, Boyes J, Chung J, Clark D, & Studitsky V. (1996) Chromatin structure and gene expression. Proceedings of the National Academy of Sciences of the United States of America, 93(18), 9384-8. PMID: 8790338
- November 17, 2012
- 12:02 PM
- 199 views
The chemistry of DNA modifications for gene regulation
by egonw in Chem-bla-ics
I have started learning about epigenetics, and particularly the regulatory effects of DNA methylation and acetylation. It's cool, it's hot, it's everything we hope will explain genetics, because genes certainly did not.
The chemistry behind this involves interesting pathways, involves storage of information that passes from one generation to another... epigenetic effects down to the grandchild generation have repeatedly been shown now. I likely candidate are mRNAs that persist beyond the cell d........ Read more »
Donohoe, D., Collins, L., Wali, A., Bigler, R., Sun, W., & Bultman, S. (2012) The Warburg Effect Dictates the Mechanism of Butyrate-Mediated Histone Acetylation and Cell Proliferation. Molecular Cell. DOI: 10.1016/j.molcel.2012.08.033
- September 22, 2012
- 11:02 AM
- 373 views
OMG! An Open Molecule Generator!
by egonw in Chem-bla-ics
Earlier this week an important cheminformatics paper appeared in the Journal of Cheminformatics. It is about the Open Molecule Generator (see below for the paper). This was one important piece of functionality still missing from Open Source cheminformatics. This works uses the Chemistry Development Kit, and was written by Julio Peironcely.
The Analytical Biosciences' group of Prof. Hankemeier (and many others, including also Theo Reijmers) and funded by the Netherlands Metab........ Read more »
Julio E Peironcely, Miguel Rojas-Chertó, Davide Fichera, Theo Reijmers, Leon Coulier, Jean-Loup Faulon, & Thomas Hankemeier. (2012) OMG: open molecule generator. Journal of Cheminformatics, 21. DOI: 10.1186/1758-2946-4-21
- April 7, 2012
- 04:47 AM
- 470 views
A typical QSAR study (cite:citesAsAuthority)
by egonw in Chem-bla-ics
I use CiTO to keep track of how the CDK is cited and used, and just looked at a typical QSAR paper. Here are my comments on "Study of indole derivative inhibitors of Cytosolic phospholipase A2α based on Quantitative Structure Activity Relationship", by Lu et al (doi:10.1016/j.chemolab.2011.11.011). Normally, I am fairly short in these reviews which I publish via the CDK Google+ page, briefly describing what CDK functionality is being used. But this time the post became a more substantial r........ Read more »
Lu, X., Ji, D., Chen, J., Zhou, X., & Shi, H. (2012) Study of indole derivative inhibitors of Cytosolic phospholipase A2α based on Quantitative Structure Activity Relationship. Chemometrics and Intelligent Laboratory Systems. DOI: 10.1016/j.chemolab.2011.11.011
- October 18, 2011
- 04:53 AM
- 532 views
The Blue Obelisk Shoulders for Translational Cheminformatics
by egonw in Chem-bla-ics
I guess reader of my blog already heard about it via other channels (e.g. via Noel's blog post), but our second Blue Obelisk paper is out. In the past five-ish years since Peter instantiated this initiative, it has created a solid set of shoulder on which to developed Open Source-based cheminformatics solutions. I created the following diagram for the paper, showing how various Blue Obelisk projects interoperate (image is CC-BY, from the paper):
It shows a number of Open Standards (diamonds)........ Read more »
Guha, R., Howard, M., Hutchison, G., Murray-Rust, P., Rzepa, H., Steinbeck, C., Wegner, J., & Willighagen, E. (2006) The Blue ObeliskInteroperability in Chemical Informatics. Journal of Chemical Information and Modeling, 46(3), 991-998. DOI: 10.1021/ci050400b
O'Boyle NM, Guha R, Willighagen EL, Adams SE, Alvarsson J, Bradley JC, Filippov IV, Hanson RM, Hanwell MD, Hutchison GR.... (2011) Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. Journal of cheminformatics, 3(1), 37. PMID: 21999342
- October 9, 2011
- 02:46 AM
- 704 views
An ontology for QSAR and cheminformatics
by egonw in Chem-bla-ics
QSAR and QSPR are the fields that statistically correlate chemical substance features with (biological) activities (QSAR) or properties (QSPR). The chemical substance can be molecular structures, drug (which are not uncommonly mixtures), and true mixture like nanomaterials (NanoQSAR). Readers of this blog know I have been working towards making these kind of studies more reproducible for many years now.
Parts of this full story include the Blue Obelisk Data Repository (BODR), QSAR-ML, the CDK f........ Read more »
Hastings, J., Chepelev, L., Willighagen, E., Adams, N., Steinbeck, C., & Dumontier, M. (2011) The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web. PLoS ONE, 6(10). DOI: 10.1371/journal.pone.0025513
- July 13, 2011
- 06:58 AM
- 1,176 views
CDK Forks
by egonw in Chem-bla-ics
Forking is an important part of Open Source development, and forking is good. Of course, forks should interact too, and genes from one fork should merge back into another fork. Forks are probably also a good indication for the success of a project: if a project is forked, it means it is significant. On the other hand, it can also mean that the main project is too hard to work with. Maybe the CDK is that. Indeed, it's easier to not have your code peer-reviewed, and just fork. That is freedom. (........ Read more »
Jeliazkova, N., & Jeliazkov, V. (2011) AMBIT RESTful web services: an implementation of the OpenTox application programming interface. Journal of Cheminformatics, 3(1), 18. DOI: 10.1186/1758-2946-3-18
Wetzel, S., Klein, K., Renner, S., Rauh, D., Oprea, T., Mutzel, P., & Waldmann, H. (2009) Interactive exploration of chemical space with Scaffold Hunter. Nature Chemical Biology, 5(8), 581-583. DOI: 10.1038/nchembio.187
Yap, C. (2011) PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints. Journal of Computational Chemistry, 32(7), 1466-1474. DOI: 10.1002/jcc.21707
- June 17, 2011
- 04:03 PM
- 1,370 views
Fast Calculation of van der Waals Volume as a Sum of Atomic and Bond Contributions
by egonw in Chem-bla-ics
I was recently asked about a volume descriptor in Bioclipse, which is not yet available. Jmol can calculate surfaces, so that was my first thought. However, I then ran into a paper from 2003 by Zhao, called Fast Calculation of van der Waals Volume as a Sum of Atomic and Bond Contributions and Its Application to Drug Compounds (doi:10.1021/jo034808o).
The paper presents a very simple mathematical model, which approximates the molecular volume by a sum of atomic contributions, and a three terms t........ Read more »
Zhao, Y., Abraham, M., & Zissimos, A. (2003) Fast Calculation of van der Waals Volume as a Sum of Atomic and Bond Contributions and Its Application to Drug Compounds. The Journal of Organic Chemistry, 68(19), 7368-7373. DOI: 10.1021/jo034808o
- March 8, 2011
- 07:40 AM
- 1,069 views
ToxBank: a data warehouse for (computational) toxicology
by egonw in Chem-bla-ics
Last week I was in sunny Cascais, and in three days experienced -23oC and +18oC. The reason I was there was the kick-off meeting of the EU FP7 cluster SEURAT, which includes 'our' ToxBank project.
Data types we will host include many different types, including my favorite metabolomics. Don't ask me what this will practically mean, but some keywords we already know include RDF, OpenTox, and ToxML. With metabolomics, I hope to squeeze in metabolomics.
And that data warehousing for metabolo........ Read more »
Bais, H., Prithiviraj, B., Jha, A., Ausubel, F., & Vivanco, J. (2005) Mediation of pathogen resistance by exudation of antimicrobials from roots. Nature, 434(7030), 217-221. DOI: 10.1038/nature03356
Walker, T., Bais, H., Halligan, K., Stermitz, F., & Vivanco, J. (2003) Metabolic Profiling of Root Exudates of . Journal of Agricultural and Food Chemistry, 51(9), 2548-2554. DOI: 10.1021/jf021166h
- February 9, 2011
- 02:01 AM
- 1,115 views
Chemical data curation: yes, it is that bad.
by egonw in Chem-bla-ics
The readers of Antony's blog know enough about the problem. And many in the QSAR community know it too (and many other do not). Chemical structure data is noisy. I haven't recently created a new local data set for analysis, so I have not taken time to blog about it much, but the ambiguity in chemical databases is enormous. Just yesterday, Antony and I had a good discussion about tautomers and in particular how things are linked together.
If we are in the field of property prediction, knowing wh........ Read more »
Porter, W. (2010) Warfarin: history, tautomerism and activity. Journal of Computer-Aided Molecular Design, 24(6-7), 553-573. DOI: 10.1007/s10822-010-9335-7
- December 26, 2010
- 10:37 AM
- 816 views
Oscar: training data, models, etc
by egonw in Chem-bla-ics
Oscar uses a Maximum Entropy Markov Model (MEMM) based on n-grams. Peter Corbett has written this up (doi:10.1186/1471-2105-9-S11-S4). So, it basically is statistics once more. If you really want a proper bioinformatics education, so do your PhD at a (proteo)chemometrics department.
N-grams are word parts of n characters. For example, the trigrams of acetic acid include ace, cid, tic, eti, and aci. N-grams of length four include acid, etic, and acet. The MEMM assigns weights to these n-grams, a........ Read more »
Corbett, P., & Copestake, A. (2008) Cascaded classifiers for confidence-based chemical named entity recognition. BMC Bioinformatics, 9(Suppl 11). DOI: 10.1186/1471-2105-9-S11-S4
- December 21, 2010
- 04:22 AM
- 614 views
re: Commercial or Proprietary?
by egonw in Chem-bla-ics
OK, the second paper I ran into today is a perfect match for the paper by Khanna and Ranganathan I just dicussed in the Commercial or Proprietary? post. So perfect, in fact, that it I should have really combined them. But since the other post is already infecting the WWW, I'll have to post this update.
Yap wrote up a paper on PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints (doi:10.1002/jcc.21707), and Table 2 is quite like Table 1 in the paper by Kh........ Read more »
Yap, C. (2010) PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints. Journal of Computational Chemistry. DOI: 10.1002/jcc.21707
- December 11, 2010
- 03:21 PM
- 1,081 views
Supramolecular chemistry
by egonw in Chem-bla-ics
Some smart software developer once said to not optimize your code too early. However, not caring about it at all does not help either. Some basic knowledge of memory management can keep you going. That is, I just ran into the limits of Oscar and ChemicalTagger. As I blogged earlier today, I am analyzing the BJOC literature, but Lezan and I are running into a reproducible out-of-memory exception. At first I thought it was a memory leak, as it was the 95th paper if fell over on, but after we optim........ Read more »
Späth, A., & König, B. (2010) Molecular recognition of organic ammonium-ions in solution using synthetic receptors. Beilstein Journal of Organic Chemistry. DOI: 10.3762/bjoc.6.32
Buijnsters, P. J. J. A.; García-Rodríguez, C. L.; Willighagen, E. L.; Sommerdijk, N. A. J. M.; Kremer, A.; Camilleri, P.; Feiters, M. C.; Nolte, R. J. M.; Zwanenburg, B. (2002) Cationic Gemini Surfactants Based on Tartaric Acid: Synthesis, Aggregation, Monolayer Behaviour, and Interaction with DNA. European Journal of Organic Chemistry, 2002(8), 1397-1406. info:/10.1002/1099-0690(200204)2002:83.0.CO;2-6
- November 27, 2010
- 06:27 AM
- 831 views
Uppsala Status Report
by egonw in Chem-bla-ics
As you know, my post-doc in Uppsala ended. It was a good time, and it was great collaborating on Bioclipse with Ola, Jonathan, Arvid, and Carl. I would have loved tighter integration with the work of Maris and Martin, but that was limited to one joined paper (in press). I thank Professors Jarl Wikberg and Eva Brittebo for allowing me to continue my research at their department, and hope this is not the end of the collaboration yet.
Like with new year, the end of a contract is a good time to ref........ Read more »
Wagener, J., Spjuth, O., Willighagen, E., & Wikberg, J. (2009) XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services. BMC Bioinformatics, 10(1), 279. DOI: 10.1186/1471-2105-10-279
Spjuth, O., Alvarsson, J., Berg, A., Eklund, M., Kuhn, S., Mäsak, C., Torrance, G., Wagener, J., Willighagen, E., Steinbeck, C.... (2009) Bioclipse 2: A scriptable integration platform for the life sciences. BMC Bioinformatics, 10(1), 397. DOI: 10.1186/1471-2105-10-397
Spjuth, O., Willighagen, E., Guha, R., Eklund, M., & Wikberg, J. (2010) Towards interoperable and reproducible QSAR analyses: Exchange of datasets. Journal of Cheminformatics, 2(1), 5. DOI: 10.1186/1758-2946-2-5
- October 16, 2010
- 04:52 AM
- 1,064 views
Royce Murray and Caveat Emptor
by egonw in Chem-bla-ics
Derek's blog pointed me to an editorial by Royce Murray Science Blogs and Caveat Emptor (doi:10.1021/ac102628p). He is warning us, science scholars, for blogs. He is accusing bloggers for not being scholarly, not checking facts etc.
He did himself and the journal a big disfavor: in his blog he does precisely what he is accusing the blogger of: fail to check facts. Even worse, particularly for the 'Analytical Chemistry' journal, he showed inadequate in analyzing the problem, putting his scholarl........ Read more »
Murray R. (2010) Science Blogs and Caveat Emptor. Analytical chemistry. PMID: 20939598
- June 20, 2010
- 11:47 AM
- 969 views
Looking at your statistical models...
by egonw in Chem-bla-ics
I do not think I have ever blogged the paper that played an important role in my thesis (doi:10.1021/ci990038z); research of one of the papers in my thesis, started with the hypothesis proposed therein. The paper had a really good idea; but, unfortunately, it did not contain the data to support the hypothesis. That gets me to one important lesson I learned: a QSAR data set of less than 100 molecules is not enough to make untargeted statistical models.
The paper reads quite nicely, and the resul........ Read more »
Bursi, R., Dao, T., van Wijk, T., de Gooyer, M., Kellenbach, E., & Verwer, P. (1999) Comparative Spectra Analysis (CoSA): Spectra as Three-Dimensional Molecular Descriptors for the Prediction of Biological Activities. Journal of Chemical Information and Modeling, 39(5), 861-867. DOI: 10.1021/ci990038z
Willighagen, E., Denissen, H., Wehrens, R., & Buydens, L. (2006) On the Use of H and C 1D NMR Spectra as QSPR Descriptors . Journal of Chemical Information and Modeling, 46(2), 487-494. DOI: 10.1021/ci050282s
- April 18, 2010
- 08:00 AM
- 1,002 views
BitTorrents for Science
by egonw in Chem-bla-ics
The idea has been lingering in the air for a long time now: sharing large science data sets using bittorrent. Over the past couple of years I have seen a lot of science related software being distributed over torrents, and the use in open source in general is abundant. Given a good network of so-called seeders, download times go down dramatically, and the overall energy consumption goes down too, as data has to follow a much shorter path.
It could very well be that the uptake of this technology........ Read more »
Langille, M., & Eisen, J. (2010) BioTorrents: A File Sharing Service for Scientific Data. PLoS ONE, 5(4). DOI: 10.1371/journal.pone.0010071
- March 11, 2010
- 07:11 AM
- 510 views
Review of Towards pharmacogenomics knowledge discovery with the semantic web
by UUCJC in Uppsala University Cheminformatics Journal Club
The article, Towards pharmacogenomics knowledge discovery with the semantic web, written by Michael Dumontier and Natalia Villanueva-Rosales attempts to demonstrate the importance of pharmacogenomics and how the data should be structured in the best possible way. Their strategy towards knowledge discovery involves ontology design, population and question answering. In a more specific manner this was established with Web Ontology Language OWL-DL, Protégé and Manchester OWL Syntax.With the SO-Ph........ Read more »
Dumontier, M., & Villanueva-Rosales, N. (2009) Towards pharmacogenomics knowledge discovery with the semantic web. Briefings in Bioinformatics, 10(2), 153-163. DOI: 10.1093/bib/bbn056
- March 1, 2008
- 05:00 AM
- 1,322 views
Jane, find me interesting journals, please.
by egonw in Chem-bla-ics
Bioinformatics just published a paper from Schuemie and Kors (Erasmus University/NL, BioSemantics group): Jane: suggesting journals, finding experts (doi:10.1093/bioinformatics/btn006):Jane (Journal/Author Name Estimator) is a freely available web-based application that, on the basis of a sample text (e.g. the title and abstract of a manuscript), can suggest journals and experts who have published similar articles.Having just gone into a different research field, I appreciate Jane as a useful to........ Read more »
M Schuemie, & J A Kors. (2008) Jane: suggesting journals, finding experts. Bioinformatics, 24(5), 727-728. DOI: 10.1093/bioinformatics/btn006
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