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Egon Willighagen › Comments

Mr. Gunn
MrGunn on We are EFF, Creative Commons, Right to Research Coalition, Open Access Button, and Fundación Karisma, and We’re Here to Answer Your Questions About Open Access. AUA! - http://www.reddit.com/r...
"Speaking as a person who is employed by Elsevier (on the product side, not the journals side, and not speaking for Elsevier as a whole), I think I'm just trying to get a product out that solves a problem for researchers. I think many of us see rights restrictions as a hindrance to product development. Having to have a rights management system built into everything causes us to incur a development cost and makes it harder to prototype and test new ideas. However, the current business model is what fuels our development, so what it comes down to is that the company does some good, but also does some things that probably wouldn't be good if we were to reinvent the scholarly publishing system from the ground up, post-Internet. Each person has to answer the question about what they think is morally acceptable for themselves, but most people who engage in a grown-up form of moral reasoning can get beyond a dualistic moral stance and accept that like most things in life, there's some good..." - Mr. Gunn
Mr. Gunn, I do not think that using "grown-up" in your argumentation is very helpful. Regarding the less good things of Elsevier, is despite their huge profits they refuse to invest in anger in new technologies, new paradigms. That is, it indeed fuels development, but just a small bit, and most goes as profit to the owners. If you really want to play the moral reasoning side of this,... more... - Egon Willighagen
Egon Willighagen
Ligand-Based Target Prediction with Signature Fingerprints - http://www.citeulike.org/user...
J. Chem. Inf. Model., Vol. 54, No. 10. (17 September 2014), pp. 2647-2653, doi:10.1021/ci500361u When evaluating a potential drug candidate it is desirable to predict target interactions in silico prior to synthesis in order to assess, e.g., secondary pharmacology. This can be done by looking at known target binding profiles of similar compounds using chemical similarity searching. The purpose of this study was to construct and evaluate the performance of chemical fingerprints based on the molecular signature descriptor for performing target binding predictions. For the comparison we used the area under the receiver operating characteristics curve (AUC) complemented with net reclassification improvement (NRI). We created two open source signature fingerprints, a bit and a count version, and evaluated their performance compared to a set of established fingerprints with regards to predictions of binding targets using Tanimoto-based similarity searching on publicly available data sets... - Egon Willighagen
Egon Willighagen
Benchmarking Study of Parameter Variation when Using Signature Fingerprints together with Support Vector Machines - http://www.citeulike.org/user...
J. Chem. Inf. Model. (15 October 2014), doi:10.1021/ci500344v QSAR modeling using molecular signatures and support vector machines with a radial basis function is increasingly used for virtual screening in the drug discovery field. This method has three free parameters: C, ? and signature height. C is a penalty parameter which limits over-fitting, ? controls the width of the radial basis function kernel and signature height determines how much of the molecule is described by each atom signature. Determination of optimal values for these parameters is time consuming. Good default values could therefore save considerable computational cost. The goal of this project was to investigate whether or not such default values could be found, by using seven public QSAR datasets spanning a wide range of endpoints and using both a bit and a count version of the molecular signatures. Based on the experiments performed, we recommend a parameter set up of heights 0 to 2 for the count version of the... - Egon Willighagen
Egon Willighagen
Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis - http://www.citeulike.org/user...
Cell, Vol. 159, No. 3. (26 October 2014), pp. 514-529, doi:10.1016/j.cell.2014.09.048 All domains of life feature diverse molecular clock machineries that synchronize physiological processes to diurnal environmental fluctuations. However, no mechanisms are known to cross-regulate prokaryotic and eukaryotic circadian rhythms in multikingdom ecosystems. Here, we show that the intestinal microbiota, in both mice and humans, exhibits diurnal oscillations that are influenced by feeding rhythms, leading to time-specific compositional and functional profiles over the course of a day. Ablation of host molecular clock components or induction of jet lag leads to aberrant microbiota diurnal fluctuations and dysbiosis, driven by impaired feeding rhythmicity. Consequently, jet-lag-induced dysbiosis in both mice and humans promotes glucose intolerance and obesity that are transferrable to germ-free mice upon fecal transplantation. Together, these findings provide evidence of coordinated... - Egon Willighagen
Egon Willighagen
Sitting down with Noureddin to talk about QSAR and looking at the OECD eChemPortal, and we just found a data bug, mixing up SMILES and InChI. - Egon Willighagen
Egon Willighagen
From Wikipedia. Last week I gave an invited presentation in the nice library of the Royal Society of Chemistry, at the What's in a Name? The Unsung Heroes of Open Innovation: Nomenclature and Terminology meeting. I was asked ... - Egon Willighagen
Egon Willighagen
The Application of Chemical Multipurpose Internet Mail Extensions (Chemical MIME) Internet Standards to Electronic Mail and World Wide Web Information Exchange - http://www.citeulike.org/user...
J. Chem. Inf. Comput. Sci., Vol. 38, No. 6. (14 August 1998), pp. 976-982, doi:10.1021/ci9803233 The proposal and subsequent global use of an Internet standard based on chemical primary Multipurpose Internet Mail Extensions (chemical MIME) media type is reviewed. Examples of the configuration of this standard for use with Internet-based electronic mail and World Wide Web clients are shown. The long-term objectives of the integration and interoperability of chemical information across the boundaries of Internet-based electronic journals, conferences, virtual courses, databases, modeling, and newly emerging information handling and modeling tools are set out. We believe that one way forward is by concentrating on more finely grained chemical information components, using generic tools based on XML (eXtensible markup language) and its support in chemistry via CML (chemical markup language). Henry Rzepa, Peter Murray-Rust, Benjamin Whitaker - Egon Willighagen
Egon Willighagen
The history of the Woordenboek Organische Chemie Chemistry students at the Radboud University in Nijmegen... - https://plus.google.com/1041867...
The history of the Woordenboek Organische Chemie Chemistry students at the Radboud University in Nijmegen (then called the Catholic University of Nijmegen ) got internet access in spring 1994. BTW, the catholic part only was reflected in the curriculum in that philosophy was an obligatory course. The inte... Chemistry students at the Radboud University in Nijmegen (then called the Catholic University of Nijmegen) got internet access in spring 1994. BTW, the catholic part only was reflected in the curriculum in that philosophy was... - Egon Willighagen
Egon Willighagen
German summary: Der wunderbaren Wikidata-Community ist es zu verdanken, dass jedes menschliche Gen (laut dem United States National Center for Biotechnology Information) jetzt durch einen Eintrag auf ... - Egon Willighagen
Egon Willighagen
Reshared post from PHD Comics: - https://plus.google.com/1041867...
How timely... Original Post from PHD Comics: Time spent in Meetings vs YOUR CAREER http://www.phdcomics.com/comics... **Hey, be part of the new PHD Movie! Click here: http://goo.gl/forms... Link to Piled Higher and Deeper - Egon Willighagen
Egon Willighagen
The ‘digital natives’ debate: A critical review of the evidence - http://www.citeulike.org/user...
British Journal of Educational Technology, Vol. 39, No. 5. (1 September 2008), pp. 775-786, doi:10.1111/j.1467-8535.2007.00793.x The idea that a new generation of students is entering the education system has excited recent attention among educators and education commentators. Termed ‘digital natives’ or the ‘Net generation’, these young people are said to have been immersed in technology all their lives, imbuing them with sophisticated technical skills and learning preferences for which traditional education is unprepared. Grand claims are being made about the nature of this generational change and about the urgent necessity for educational reform in response. A sense of impending crisis pervades this debate. However, the actual situation is far from clear. In this paper, the authors draw on the fields of education and sociology to analyse the digital natives debate. The paper presents and questions the main claims made about digital natives and analyses the nature of the debate... - Egon Willighagen
Egon Willighagen
Impactstory team, you need to check your G+ account name. Maybe it is the space, but something of your... - https://plus.google.com/1041867...
Impactstory team, you need to check your G+ account name. Maybe it is the space, but something of your account is breaking mentioning the account inline in G+... I tried this at the start of this message, and as you can see, it is not linked, even though it did recognize it at first, allowing me to select the account, but no link gets created...  - Egon Willighagen
Egon Willighagen
That should make an interesting read! I personally do not believe in this "digital natives" generation... - https://plus.google.com/1041867...
That should make an interesting read! I personally do not believe in this "digital natives" generation... all modern hardware makes it way too easy to not care about how it works. Tables, smartphones, etc are about brainless consumption and not about thinking about things. Sue Bennett, Karl Maton, Lisa Kervin. British Journal of Educational Technology, Vol. 39, No. 5. (1 September 2008), pp. 775-786, doi:10.1111/j.1467-8535.2007.00793.x. The idea that a new generation of students is entering the education system has excited recent attention among educators and education commentators. Termed ‘digital natives’ or the ‘Net generation’, these young people are said to have been immersed in technology all their lives, im... - Egon Willighagen
Egon Willighagen
Reshared post from Jan Jensen: - https://plus.google.com/1041867...
Original Post from Jan Jensen: 100K views on my YouTube channel I passed the 100,000 views mark on my YouTube channel . That's not very much by YouTube standards but I'm still surprised given the pretty dry videos I tend to make.  Most of these videos were made for teaching of some kind, so I am happy that a few other f... I passed the 100000 views mark on my YouTube channel. That's not very much by YouTube standards but I'm still surprised given the pretty dry videos I tend to make. Most of these videos were made for teaching of some kind, so I am happy that a few other folks found them useful. - Egon Willighagen
Egon Willighagen
Egonw: {{multiple issues| {{Cleanup-spam|date=August 2013}} {{Cleanup-list|date=August 2013}}}} A '''molecule editor''' is a [[computer program]] for creating and modifying representations of [[chemical structure]]s. Molecule editors can manipulate chemical structure representations in either two- or three-dimensions. [[Two-dimensional]] editors generate output used as illustrations or for querying [[chemical database]]s. [[3-D computer graphics|Three-dimensional]] molecule editors are used to build molecular models, usually as part of [[molecular modelling]] software packages. Database molecular editors such as Leatherface,<ref>Kenny, P.W.; Sadowski, J. (2005) [http://dx.doi.org/10... Structure modification in chemical databases] ''Chemoinformatics in drug discovery'' (editor&mdash;Oprea, T.I.), 271-285 (Wiley).</ref> RECAP<ref>Lewell, X.Q.; Judd, D.B; Watson, S.P.; Hann, M.M. (1998) [http://dx.doi.org/10... RECAP-Retrosynthetic Combinatorial Analysis... - Egon Willighagen
Egon Willighagen
CyTargetLinker: A Cytoscape App to Integrate Regulatory Interactions in Network Analysis - http://www.citeulike.org/user...
PLoS ONE, Vol. 8, No. 12. (5 December 2013), e82160, doi:10.1371/journal.pone.0082160 The high complexity and dynamic nature of the regulation of gene expression, protein synthesis, and protein activity pose a challenge to fully understand the cellular machinery. By deciphering the role of important players, including transcription factors, microRNAs, or small molecules, a better understanding of key regulatory processes can be obtained. Various databases contain information on the interactions of regulators with their targets for different organisms, data recently being extended with the results of the ENCODE (Encyclopedia of DNA Elements) project. A systems biology approach integrating our understanding on different regulators is essential in interpreting the regulation of molecular biological processes. We developed CyTargetLinker (http://projects.bigcat.unimaas.nl/cytarg etlinker), a Cytoscape app, for integrating regulatory interactions in network analysis. Recently we released... - Egon Willighagen
Egon Willighagen
Bioinformatics, Vol. 29, No. 10. (15 May 2013), pp. 1350-1351, doi:10.1093/bioinformatics/btt138 Summary: Cytoscape is an open source software tool for biological network visualization and analysis, which can be extended with independently developed apps. We launched the Cytoscape App Store to highlight the important features that apps add to Cytoscape, enable researchers to find and install apps they need and help developers promote their apps. Samad Lotia, Jason Montojo, Yue Dong, Gary Bader, Alexander Pico - Egon Willighagen
Egon Willighagen
In Chemometrics with R (2011), doi:10.1007/978-3-642-17841-2 Ron Wehrens - Egon Willighagen
Egon Willighagen
Uncovering global SUMOylation signaling networks in a site-specific manner - http://www.citeulike.org/user...
Nature Structural &#38; Molecular Biology, Vol. 21, No. 10. (14 September 2014), pp. 927-936, doi:10.1038/nsmb.2890 High-resolution MS identifies >4,300 SUMOylation sites in >1,600 proteins in human cells under standard growth conditions and after proteasome inhibition or heat shock. The data reveal cross-talk between SUMO and other post-translational modifications. Ivo Hendriks, Rochelle D'Souza, Bing Yang, Matty Verlaan-de Vries, Matthias Mann, Alfred Vertegaal - Egon Willighagen
Egon Willighagen
Accessing biological data in R with semantic web technologies - http://www.citeulike.org/user...
PeerJ PrePrints (31 December 2013), doi:10.7287/peerj.preprints.185 Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness shows advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows. Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be used in the statistical environment R. The code is exposed as two R packages available from the Comprehensive R Archive Network (CRAN). The RJava library and a custom convenience class is used to bridge between R and the Jena library. Results. We here present three examples showing how the Resource Description Framework (RDF) and SPARQL query standards can be employed in R. The first example takes input on BRCA1 SNPs from a... - Egon Willighagen
Egon Willighagen
Egon Willighagen
Obesity accelerates epigenetic aging of human liver - http://www.citeulike.org/user...
Proceedings of the National Academy of Sciences (13 October 2014), 201412759, doi:10.1073/pnas.1412759111 Steve Horvath, Wiebke Erhart, Mario Brosch, Ole Ammerpohl, Witigo von Schönfels, Markus Ahrens, Nils Heits, Jordana Bell, Pei-Chien Tsai, Tim Spector, Panos Deloukas, Reiner Siebert, Bence Sipos, Thomas Becker, Christoph Röcken, Clemens Schafmayer, Jochen Hampe - Egon Willighagen
Egon Willighagen
Visual Workflows for 13C-Metabolic Flux Analysis - http://www.citeulike.org/user...
Bioinformatics (7 October 2014), doi:10.1093/bioinformatics/btu585 Motivation: The precise quantification of intracellular metabolic flow rates is of fundamental importance in bio(techno)logy and medical research. The gold standard in the field is metabolic flux analysis (MFA) with 13C-labeling experiments. 13C-MFA workflows orchestrate several, mainly human-in-the-loop software applications, integrating them with plenty of heterogeneous information. In practice, this had posed a major practical barrier for evaluating, interpreting, and understanding isotopic data from carbon labeling experiments.Results: Graphical modeling, interactive model exploration, and visual data analysis are the key to overcome this limitation. We have developed a first-of-its-kind graphical tool suite providing scientists with an integrated software framework for all aspects of 13C-MFA. Almost 30 modules (plugins) have been implemented for the Omix visualization software. Several advanced graphical workflows... - Egon Willighagen
Egon Willighagen
Long-echo time MR spectroscopy for skeletal muscle acetylcarnitine detection. - http://www.citeulike.org/user...
The Journal of clinical investigation (1 October 2014) Animal models suggest that acetylcarnitine production is essential for maintaining metabolic flexibility and insulin sensitivity. Because current methods to detect acetylcarnitine involve biopsy of the tissue of interest, noninvasive alternatives to measure acetylcarnitine concentrations could facilitate our understanding of its physiological relevance in humans. Here, we investigated the use of long-echo time (TE) proton magnetic resonance spectroscopy (1H-MRS) to measure skeletal muscle acetylcarnitine concentrations on a clinical 3T scanner. We applied long-TE 1H-MRS to measure acetylcarnitine in endurance-trained athletes, lean and obese sedentary subjects, and type 2 diabetes mellitus (T2DM) patients to cover a wide spectrum in insulin sensitivity. A long-TE 1H-MRS protocol was implemented for successful detection of skeletal muscle acetylcarnitine in these individuals. There were pronounced differences in insulin... - Egon Willighagen
Egon Willighagen
Scientific Lenses to Support Multiple Views over Linked Chemistry Data - http://www.citeulike.org/user...
In The Semantic Web – ISWC 2014, Vol. 8796 (2014), pp. 98-113, doi:10.1007/978-3-319-11964-9_7 When are two entries about a small molecule in different datasets the same? If they have the same drug name, chemical structure, or some other criteria? The choice depends upon the application to which the data will be put. However, existing Linked Data approaches provide a single global view over the data with no way of varying the notion of equivalence to be applied. In this paper, we present an approach to enable applications to choose the equivalence criteria to apply between datasets. Thus, supporting multiple dynamic views over the Linked Data. For chemical data, we show that multiple sets of links can be automatically generated according to different equivalence criteria and published with semantic descriptions capturing their context and interpretation. This approach has been applied within a large scale public-private data integration platform for drug discovery. To cater for... - Egon Willighagen
Egon Willighagen
Reshared post from Graham Steel: - https://plus.google.com/1041867...
This is not a reincarnation of the fake DOI? Original Post from Graham Steel: Elsevier are now charging $30 for blank PDF's. http://www.sciencedirect.com/science... blankpage2.png - Egon Willighagen
Egon Willighagen
This page is intentionally left blank - http://www.citeulike.org/user...
In Verified Syntheses of Zeolitic Materials (2001), 267, doi:10.1016/b978-044450703-7/50187-3 - Egon Willighagen
Egon Willighagen
2014 update! Well done! This web page is the home of the LOD cloud diagram. This image shows datasets that have been published in Linked Data format, by contributors to the Linking Open Data community project and other individuals and organisations. It is based on metadata collected and curated by contributors to the ... - Egon Willighagen
Egon Willighagen
Reshared post from NextMove Software: - https://plus.google.com/1041867...
Excellent post showing that data analysis requires thinking about how you represent your problem. In other words, it really matters how you represent your data, what analysis you can do, and therefore, what hypothesis you can answer. Original Post from NextMove Software: If we know some activity orders as a starting point, our ability to predict is much improved... There is a 2008 paper by the folks at Abbott that Roger refers to as “the paper that killed matched pairs for activity data”. This is the Hajduk and Sauer paper which looked at matched pair transformations across 84K compounds and 30 protein targets, and found that the potency changes associated ... - Egon Willighagen
Egon Willighagen
Me is thinking old editions of the CRC Handbook of Chemistry and Physics... - https://plus.google.com/1041867...
Me is thinking old editions of the CRC Handbook of Chemistry and Physics... Announcing BookLiberator Beta — the affordable, low-tech book digitizer that's made of wood, looks good in your living room or library, and can scan 600-900 pages per hour! Order now from our online store. We're very pleased to announce the availability of BookLiberator Beta kits. - Egon Willighagen
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