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Egon Willighagen › Comments

Egon Willighagen
TrkB-Mediated Protection against Circadian Sensitivity to Noise Trauma in the Murine Cochlea - http://www.citeulike.org/user...
Current Biology (February 2014), doi:10.1016/j.cub.2014.01.047 Inna Meltser, Christopher Cederroth, Vasiliki Basinou, Sergey Savelyev, Gabriella Lundkvist, Barbara Canlon - Egon Willighagen
Egon Willighagen
Type 2 diabetes as a redox disease - http://www.citeulike.org/user...
The Lancet, Vol. 383, No. 9919. (March 2014), pp. 841-843, doi:10.1016/s0140-6736(13)62365-x James Watson - Egon Willighagen
Egon Willighagen
A Selected Core Microbiome Drives the Early Stages of Three Popular Italian Cheese Manufactures - http://www.citeulike.org/user...
PLoS ONE, Vol. 9, No. 2. (24 February 2014), e89680, doi:10.1371/journal.pone.0089680 Mozzarella (M), Grana Padano (GP) and Parmigiano Reggiano (PR) are three of the most important traditional Italian cheeses. In the three cheese manufactures the initial fermentation is carried out by adding natural whey cultures (NWCs) according to a back-slopping procedure. In this study, NWCs and the corresponding curds from M, GP and PR manufactures were analyzed by culture-independent pyrosequencing of the amplified V1–V3 regions of the 16S rRNA gene, in order to provide insights into the microbiota involved in the curd acidification. Moreover, culture-independent high-throughput sequencing of lacS gene amplicons was carried out to evaluate the biodiversity occurring within the S. thermophilus species. Beta diversity analysis showed a species-based differentiation between GP-PR and M manufactures indicating differences between the preparations. Nevertheless, all the samples shared a... - Egon Willighagen
Egon Willighagen
Extending a deadline has effect. The question is, is the extra attention a deadline gets the reason ... - https://plus.google.com/1041867...
Extending a deadline has effect. The question is, is the extra attention a deadline gets the reason for more interest, causing the second steep rise? Are we really this busy that we cannot find enough time to hand in abstracts in time? It is going to be an exciting meeting! http://www.int-conf-chem-structures.org/  image001.png - Egon Willighagen
Egon Willighagen
Reshared post from Google Summer of Code: - https://plus.google.com/1041867...
Original Post from Google Summer of Code: The student application period for GSoC 2014 opens in a couple weeks. Here's a video of +Carol Smith explaining more about student apps. Google Summer of Code 201, Student Application Process - Egon Willighagen
Egon Willighagen
Reshared post from Marcus Hanwell: - https://plus.google.com/1041867...
Original Post from Marcus Hanwell: Who helps your Linux distribution run smoothly? Thank a packager today. They deserve it, I once did this for Gentoo! It can be a thankless task at times... The people behind the scenes who work tirelessly to make your Linux distribution run smoothly are the packagers. The vast majority of Linux packagers are volunteers who dedicate their evenings and weekends to create and maintain the gears of the Linux distributions they love. - Egon Willighagen
Egon Willighagen
Reshared post from Assignment Expert: - https://plus.google.com/1041867...
Original Post from Assignment Expert: Two species of tropical octopus have evolved a neat trick to avoid predators - they lift up six of their arms and walk backward on the other two. When walking, these octopuses use the outer halves of their two back arms like tank treads, alternately laying down a sucker edge and rolling it along the ground. In Indonesia, for example, the coconut octopus looks like a coconut tiptoeing along the ocean bottom, six of its arms wrapped tightly around its body. Crissy Huffard clocked the two-legged speed of one coconut octopus at two and a half inches per second, while a second individual zoomed along, backwards, at five and a half inches per second. This is faster than they can crawl, but probably slower than they jet around. Huffard and coauthor Robert Full, professor of integrative biology at UC Berkeley, think that this bipedal walking is a strategy octopuses use to backpedal away from predators while remaining camouflaged. Octopuses camouflage... - Egon Willighagen
Egon Willighagen
Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI) - http://www.citeulike.org/user...
PLoS ONE, Vol. 8, No. 10. (4 October 2013), e75185, doi:10.1371/journal.pone.0075185 Biomedical entities, their identifiers and names, are essential in the representation of biomedical facts and knowledge. In the same way, the complete set of biomedical and chemical terms, i.e. the biomedical “term space” (the “Lexeome”), forms a key resource to achieve the full integration of the scientific literature with biomedical data resources: any identified named entity can immediately be normalized to the correct database entry. This goal does not only require that we are aware of all existing terms, but would also profit from knowing all their senses and their semantic interpretation (ambiguities, nestedness). This study compiles a resource for lexical terms of biomedical interest in a standard format (called “LexEBI”), determines the overall number of terms, their reuse in different resources and the nestedness of terms. LexEBI comprises references for protein and gene entries and their... - Egon Willighagen
Egon Willighagen
A Chiral Gold Nanocluster Au20 Protected by Tetradentate Phosphine Ligands - http://www.citeulike.org/user...
Angew. Chem. Int. Ed. (7 February 2014), pp. n/a-n/a, doi:10.1002/anie.201308599 The chirality of a gold nanocluster can be generated from either an intrinsically chiral inorganic core or an achiral inorganic core in a chiral environment. The first structural determination of a gold nanocluster containing an intrinsic chiral inorganic core is reported. The chiral gold nanocluster [Au20(PP3)4]Cl4 (PP3=tris(2-(diphenylphosphino)ethyl)phosphine) has been prepared by the reduction of a gold(I)–tetraphosphine precursor in dichloromethane solution. Single-crystal structural determination reveals that the cluster molecular structure has C3 symmetry. It consists of a Au20 core consolidated by four peripheral tetraphosphines. The Au20 core can be viewed as the combination of an icosahedral Au13 and a helical Y-shaped Au7 motif. The identity of this Au20 cluster is confirmed by ESI-MS. The chelation of multidentate phosphines enhances the stability of this Au20 cluster. Xian-Kai Wan, Shang-Fu... - Egon Willighagen
Egon Willighagen
Elsevier's new text mining initiative is a step sideways Elsevier's new ideas on text mining are getting... - https://plus.google.com/1041867...
Elsevier's new text mining initiative is a step sideways Elsevier's new ideas on text mining are getting a lot attention now. Sadly, they get it wrong, again. On the bright side, all other publishers, which are expected to follow this year , can learn from this mistake. Because if done right, the publishers can e... I know that many will disagree on the CCZero license, and many will feel awkward about giving away data. It has value, right? It's your property, right? I am not going to argue against that. But personally I do not understand how it aligns with the idea of scientific dissemination. - Egon Willighagen
Egon Willighagen
As a student, my only dream was to solve all the grand challenges of modern biology with a computer. I confess this ambition does not really set me apart from most bioinformaticists. I also confess my success does not set me ... - Egon Willighagen
Egon Willighagen
Reshared post from Royal Society of Chemistry: - https://plus.google.com/1041867...
Original Post from Royal Society of Chemistry: Do you want to become a chemistry Wikipedia editor? Sign up for our workshop on 28 March at Burlington House, London!  You'll learn how to edit Wikipedia pages, find out about chemical information currently on Wikipedia and take part in an ‘editathon’ to generate new chemistry-related entries. If you would like to take part in the workshop visit the wiki page of the event https://wikimedia.org.uk/wiki... Wikipedia-logo-en-big.png - Egon Willighagen
Egon Willighagen
+Julio Peironcely, what is the state of a parallel OMG? Can I contribute to that by updating the code... - https://plus.google.com/1041867...
+Julio Peironcely, what is the state of a parallel OMG? Can I contribute to that by updating the code base to #CDK 1.5.x? Or is that already done? - Egon Willighagen
Egon Willighagen
eNanoMapper has a (temporary?) logo :) - https://plus.google.com/1041867...
eNanoMapper has a (temporary?) logo :) enmLogo.128x128.png - Egon Willighagen
Egon Willighagen
But at least it does not seem to insist on installing bloatware anymore... - https://plus.google.com/1041867...
But at least it does not seem to insist on installing bloatware anymore... Does that mean that I also have to approve applets on trusted domains every month?!?! - Egon Willighagen
Egon Willighagen
Scientific names of organisms: attribution, rights, and licensing - http://www.citeulike.org/user...
BMC Research Notes, Vol. 7, No. 1. (2014), 79, doi:10.1186/1756-0500-7-79 BACKGROUND:As biological disciplines extend into the 'big data' world, they will need a names-based infrastructure to index and interconnect distributed data. The infrastructure must have access to all names of all organisms if it is to manage all information. Those who compile lists of species hold different views as to the intellectual property rights that apply to the lists. This creates uncertainty that impedes the development of a much-needed infrastructure for sharing biological data in the digital world.FINDINGS:The laws in the United States of America and European Union are consistent with the position that scientific names of organisms and their compilation in checklists, classifications or taxonomic revisions are not subject to copyright. Compilations of names, such as classifications or checklists, are not creative in the sense of copyright law. Many content providers desire credit for their... - Egon Willighagen
Egon Willighagen
Can we predict top-level sports performance in power vs endurance events? A genetic approach. - http://www.citeulike.org/user...
Scandinavian journal of medicine &#38; science in sports, Vol. 21, No. 4. (August 2011), pp. 570-579, doi:10.1111/j.1600-0838.2009.01079.x The goal of our study was to discriminate potential genetic differences between humans who are in both endpoints of the sports performance continuum (i.e. world-class endurance vs power athletes). We used DNA-microarray technology that included 36 genetic variants (within 20 different genes) to compare the genetic profile obtained in two cohorts of world-class endurance (N=100) and power male athletes (N=53) of the same ethnic origin. Stepwise multivariate logistic regression showed that the rs1800795 (IL6-174 G/C), rs1208 (NAT2 K268R) and rs2070744 (NOS3-786 T/C) polymorphisms significantly predicted sport performance (model χ(2) =25.3, df=3, P-value <0.001). Receiver-operating characteristic (ROC) curve analysis showed a significant discriminating accuracy of the model, with an area under the ROC curve of 0.72 (95% confidence interval:... - Egon Willighagen
Egon Willighagen
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2 - http://www.citeulike.org/user...
Journal of Cheminformatics, Vol. 6, No. 1. (2014), 2, doi:10.1186/1758-2946-6-2 BACKGROUND:An important step in the reconstruction of a metabolic network is annotation of metabolites. Metabolites are generally annotated with various database or structure based identifiers. Metabolite annotations in metabolic reconstructions may be incorrect or incomplete and thus need to be updated prior to their use. Genome-scale metabolic reconstructions generally include hundreds of metabolites. Manually updating annotations is therefore highly laborious. This prompted us to look for open-source software applications that could facilitate automatic updating of annotations by mapping between available metabolite identifiers. We identified three applications developed for the metabolomics and chemical informatics communities as potential solutions. The applications were MetMask, the Chemical Translation System, and UniChem. The first implements a "metabolite masking" strategy for mapping between... - Egon Willighagen
Egon Willighagen
Reshared post from John May: - https://plus.google.com/1041867...
Interesting paper! And with a great impact on the recent CDK versions. Well done! Original Post from John May: Describing and measuring improved algorithms for ring (cycle) finding in the Chemistry Development Kit. The Chemistry Development Kit (CDK) is an open source Java library for manipulating and processing chemical information. A key aspect in handling chemical structures is the determination of the chemical rings. The rings of a structure are used areas including descriptors, stereochemistry, similarity, screening and atom typing. The CDK includes multiple algorithms for determining the rings of a structure on demand. Non-unique descriptions of rings... - Egon Willighagen
Egon Willighagen
Efficient ring perception for the chemistry development kit - http://www.citeulike.org/user...
Journal of Cheminformatics, Vol. 6, No. 1. (2014), 3, doi:10.1186/1758-2946-6-3 BACKGROUND:The Chemistry Development Kit (CDK) is an open source Java library for manipulating and processing chemical information. A key aspect in handling chemical structures is the determination of the chemical rings. The rings of a structure are used areas including descriptors, stereochemistry, similarity, screening and atom typing. The CDK includes multiple algorithms for determining the rings of a structure on demand. Non-unique descriptions of rings were often used due to the slower performance of the unique alternatives.RESULTS:Efficient algorithms for handling chemical ring perception have been implemented and optimised in the CDK. The algorithms provide much faster computation of new and existing types of rings. Several optimisation and implementation considerations are discussed which improve real case usage. The performance is measured on several publicly available data sets and in several... - Egon Willighagen
Egon Willighagen
Unit testing on Jenkins is working for WikiPathways curation :) - Egon Willighagen
Egon Willighagen
How to add a PubChem compound identifier to a WikiPathways … - Egon Willighagen
Egon Willighagen
Is Open Science Sweden still operating under the Open Knowledge Foundation umbrella? I do not see it... - https://plus.google.com/1041867...
Is Open Science Sweden still operating under the Open Knowledge Foundation umbrella? I do not see it listed as a Local Group at http://science.okfn.org/communi... ... - Egon Willighagen
Egon Willighagen
What Duck Duck Go returns when you search for the CDK... - https://plus.google.com/1041867...
What Duck Duck Go returns when you search for the CDK... cdkDDG.png - Egon Willighagen
Egon Willighagen
Reshared post from John May: - https://plus.google.com/1041867...
Original Post from John May: CDK release (dev) 1.5.5 - https://github.com/cdk... cdk/cdk - Egon Willighagen
Egon Willighagen
Really pleased to see that +BioMed Central now puts the graphical ToC on the abstract webpage! - https://plus.google.com/1041867...
Really pleased to see that +BioMed Central now puts the graphical ToC on the abstract webpage! Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others can link back using Uniform Resource Identifiers (URIs). RDF makes the data machine-readable and uses extensible vocabularies for additional information, making it easier to scale up inference and data analysis. - Egon Willighagen
Egon Willighagen
Testing for adaptive signatures of amino acid alphabet evolution using chemistry space - http://www.citeulike.org/user...
Journal of Systems Chemistry, Vol. 5, No. 1. (2014), 1, doi:10.1186/1759-2208-5-1 BACKGROUND:Multidisciplinary consensus indicates that half of the genetically amino acids are likely to have been available on the prebiotic earth, which implies certain adaptive expectations for the relationship between those amino acids and later additions to the genetic code. Chemistry space a concept that translates molecules to corresponding points in multidimensional space provides a framework for investigating these relationships. We therefore developed three tests to explore these implications using chemistry space to quantify otherwise qualitative questions.RESULTS:All three of our tests individually, as well as combined, provide quantitative evidence to support an adaptive expansion of the genetically encoded amino acid alphabet from 10 prebiotically plausible ("early") amino acids to the full set of 20 amino acids found within the standard genetic code.CONCLUSIONS:We present three logically... - Egon Willighagen
Egon Willighagen
"Transtition or Hell"... about the future of universities. - https://plus.google.com/1041867...
"Transtition or Hell"... about the future of universities. At the start of the discussion at Maastricht University, Frank Huisman, one of the initiators of 'Science in Transition' quickly summarized what preceded: “First we made an inventory of our personal grievances but then we grew analytical. We figured that there is something wrong with the image ... - Egon Willighagen
Egon Willighagen
Now with a +Lanyrd page (the main webpage is at: http://www.int-conf-chem-structures.org/)... deadline... - https://plus.google.com/1041867...
Now with a +Lanyrd page (the main webpage is at: http://www.int-conf-chem-structures.org/)... deadline is still January 31 to submit your work in various fields of cheminformatics. together with the 10th German Conference on Cheminformatics - Egon Willighagen
Egon Willighagen
The abstract deadline is January 31 for #iccs2014. The topics include: - Cheminformatics - Structure... - https://plus.google.com/1041867...
The abstract deadline is January 31 for #iccs2014. The topics include: - Cheminformatics - Structure-Activity and Structure-Property Prediction - Structure-Based Drug Design and Virtual Screening - Analysis of Large Chemistry Spaces - Integration of Chemical Information with other Resources - Dealing with Biological Complexity It's a wonderful meeting, and basically the place to be for cheminformations in Europe. Notice that it is a combined meeting with the German Conference on Cheminformatics this year! The Joint International Conference on Chemical Structures and the German Conference on Chemoinformatics bring together an international audience interested in handling chemical structures, cheminformatics and related topics. 10th ICCS & 10th GCC on June 1-5 2014, Noordwijkerhout, The Netherlands - Egon Willighagen
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