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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
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
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
The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web - http://dx.doi.org/10...
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
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
wikipathways: Finding consistent disease subnetworks using PFSNet. Lim K, Wong L (2014) Bioinformatics 2(30). Lim et al describe PFSNet, a tool that identifies smaller parts of pathways (subnetworks), and show that significant subnetworks (and the genes therein) discovered by PFSNet are up to 51% (64%) more consistent across independent datasets... - http://egonw.tumblr.com/post...
wikipathways:
  
Finding consistent disease subnetworks using PFSNet.
Lim K, Wong L (2014) Bioinformatics 2(30).
Lim et al describe PFSNet, a tool that identifies smaller parts of pathways (subnetworks), and show that significant subnetworks (and the genes therein) discovered by PFSNet are up to 51% (64%) more consistent across independent datasets of the same disease phenotypes, even for datasets based on different platforms, than previously published methods. PFSNet uses WikiPathways as a pathway data source.
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
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
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
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
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
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
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
+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
eNanoMapper has a (temporary?) logo :) - https://plus.google.com/1041867...
eNanoMapper has a (temporary?) logo :) enmLogo.128x128.png - 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
Does that mean that I also have to approve applets on trusted domains every month?!?! - http://egonw.tumblr.com/post...
Does that mean that I also have to approve applets on trusted domains every month?!?!
wikipathways: Whole blood transcriptome comparison of pigs with extreme production of in vivo dsRNA-induced serum IFN-a. Liu X1, Huang J2, Yang S3, Zhao Y3, Xiang A3, Cao J3, Fan B3, Wu Z4, Zhao J5, Zhao S3, Zhu M6. Dev Comp Immunol. 2013 Dec 1;44(1):35-43. Liu et al designed a transcriptomic analysis to describe the whole blood differential... - http://egonw.tumblr.com/post...
wikipathways:
  
Whole blood transcriptome comparison of pigs with extreme production of in vivo dsRNA-induced serum IFN-a.
Liu X1, Huang J2, Yang S3, Zhao Y3, Xiang A3, Cao J3, Fan B3, Wu Z4, Zhao J5, Zhao S3, Zhu M6. Dev Comp Immunol. 2013 Dec 1;44(1):35-43.
 
Liu et al designed a transcriptomic analysis to describe the whole blood differential transcriptional response to dsRNA by pigs with high vs. low IFN alpha levels. PathVisio was used to visualize the regulatory mechanism of the induction of interferon in pig cells.
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
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
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
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
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
Unit testing on Jenkins is working for WikiPathways curation :) - Egon Willighagen
Unit testing on Jenkins is working for WikiPathways curation :) - http://egonw.tumblr.com/post...
Unit testing on Jenkins is working for WikiPathways curation :)
How to add a PubChem compound identifier to a WikiPathways … - Egon Willighagen
How to add a PubChem compound identifier to a WikiPathways … - http://egonw.tumblr.com/post...
How to add a PubChem compound identifier to a WikiPathways …
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
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