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Egon Willighagen › Comments

Egon Willighagen
BridgeDb: BridgeDb 2.0.0 released - http://www.citeulike.org/user...
ZENODO (24 November 2014), doi:10.5281/zenodo.12839 CY Brenninkmeijer, E Willighagen, A Pico, M Summer-Kutmon - Egon Willighagen
Egon Willighagen
Reshared post from Jan Jensen: - https://plus.google.com/1041867...
Original Post from Jan Jensen: Computing a accessible surface area using Jmol Someone asked me how to compute a surface area of a molecule.  Here's how to compute a solvent accessible surface area using Jmol . 1. Load your molecule into Jmol (File > Open) 2. Open the Script Editor and Output Console (File > Script Editor, etc) 3. Typ... Someone asked me how to compute a surface area of a molecule. Here's how to compute a solvent accessible surface area using Jmol. 1. Load your molecule into Jmol (File > Open) 2. Open the Script Editor and Output Console (File > Script Editor, etc) 3. Type the following three lines into the ... - Egon Willighagen
Egon Willighagen
Powered by Linked Data. Only in English at this moment, it seems. Playable with ChromeCast and one or... - https://plus.google.com/1041867...
Powered by Linked Data. Only in English at this moment, it seems. Playable with ChromeCast and one or more phone/tablets behind your TV. Includes science questions. Enjoyable! - Egon Willighagen
Egon Willighagen
Egon Willighagen
Yesterday I started the Computational Chemistry Daily which aggregates posts related to computational chemistry on social media such as Twitter, Google+ and Facebook on a daily basis. It identifies the posts by certain words or hashtags such as #compchem and everyone can contribute. - Egon Willighagen
Egon Willighagen
Inroads to Predict in Vivo Toxicology—An Introduction to the eTOX Project - http://www.citeulike.org/user...
International Journal of Molecular Sciences, Vol. 13, No. 3. (21 March 2012), pp. 3820-3846, doi:10.3390/ijms13033820 There is a widespread awareness that the wealth of preclinical toxicity data that the pharmaceutical industry has generated in recent decades is not exploited as efficiently as it could be. Enhanced data availability for compound comparison (“read-across”), or for data mining to build predictive tools, should lead to a more efficient drug development process and contribute to the reduction of animal use (3Rs principle). In order to achieve these goals, a consortium approach, grouping numbers of relevant partners, is required. The eTOX (“electronic toxicity”) consortium represents such a project and is a public-private partnership within the framework of the European Innovative Medicines Initiative (IMI). The project aims at the development of in silico prediction systems for organ and in vivo toxicity. The backbone of the project will be a database consisting of... - Egon Willighagen
Egon Willighagen
The eTOX Data-Sharing Project to Advance in Silico Drug-Induced Toxicity Prediction - http://www.citeulike.org/user...
International Journal of Molecular Sciences, Vol. 15, No. 11. (14 November 2014), pp. 21136-21154, doi:10.3390/ijms151121136 The high-quality in vivo preclinical safety data produced by the pharmaceutical industry during drug development, which follows numerous strict guidelines, are mostly not available in the public domain. These safety data are sometimes published as a condensed summary for the few compounds that reach the market, but the majority of studies are never made public and are often difficult to access in an automated way, even sometimes within the owning company itself. It is evident from many academic and industrial examples, that useful data mining and model development requires large and representative data sets and careful curation of the collected data. In 2010, under the auspices of the Innovative Medicines Initiative, the eTOX project started with the objective of extracting and sharing preclinical study data from paper or pdf archives of toxicology departments... - Egon Willighagen
Egon Willighagen
Reshared post from Susanna-Assunta Sansone: - https://plus.google.com/1041867...
Original Post from Susanna-Assunta Sansone: Editorial and News: Nature and the Nature research journals are strengthening their editorial links with Scientific Data to enhance their data-availability practices! With our ISA and BioSharing work  - supporting Scientific Data - we are very glad to be part of and help with this process. Data-access practices strengthened - Egon Willighagen
Egon Willighagen
A network biology workflow to study transcriptomics data of the diabetic liver - http://www.citeulike.org/user...
BMC Genomics, Vol. 15, No. 1. (15 November 2014), 971, doi:10.1186/1471-2164-15-971 BACKGROUND:Nowadays a broad collection of transcriptomics data is publicly available in online repositories. Methods for analyzing these data often aim at deciphering the influence of gene expression at the process level. Biological pathway diagrams depict known processes and capture the interactions of gene products and metabolites, information that is essential for the computational analysis and interpretation of transcriptomics data. The present study describes a comprehensive network biology workflow that integrates differential gene expression in the human diabetic liver with pathway information by building a network of interconnected pathways. Worldwide, the incidence of type 2 diabetes mellitus is increasing dramatically, and to better understand this multifactorial disease, more insight into the concerted action of the disease-related processes is needed. The liver is a key player in metabolic... - Egon Willighagen
Egon Willighagen
Defining Molecular Initiating Events in the Adverse Outcome Pathway Framework for Risk Assessment - http://www.citeulike.org/user...
Chem. Res. Toxicol. (29 October 2014), doi:10.1021/tx500345j Consumer and environmental safety decisions are based on exposure and hazard data, interpreted using risk assessment approaches. The adverse outcome pathway (AOP) conceptual framework has been presented as a logical sequence of events or processes within biological systems which can be used to understand adverse effects and refine current risk assessment practices in ecotoxicology. This framework can also be applied to human toxicology and is explored on the basis of investigating the molecular initiating events (MIEs) of compounds. The precise definition of the MIE has yet to reach general acceptance. In this work we present a unified MIE definition: an MIE is the initial interaction between a molecule and a biomolecule or biosystem that can be causally linked to an outcome via a pathway. Case studies are presented, and issues with current definitions are addressed. With the development of a unified MIE definition, the... - Egon Willighagen
Egon Willighagen
Scientists report a new method for establishing whether chemical compounds are safe for human use without "in vivo" testing, based on so-called "molecular initiating events" at the boundary between chemistry and biology. - Egon Willighagen
Egon Willighagen
Congratulations to Pekka and Roland for their important work on alternatives for animal testing! (HT... - https://plus.google.com/1041867...
Congratulations to Pekka and Roland for their important work on alternatives for animal testing! (HT to Barry for the pointer) We are delighted to announce 12 outstanding winners of the 2014 Lush Prize Awards, sharing £250,00 in prize money. - Egon Willighagen
Egon Willighagen
Reshared post from John May: - https://plus.google.com/1041867...
Original Post from John May: Some fun with Scala's implicit methods, CDK, and RDKit. Earlier this year I wrote up some Chemical Toolkit Rosetta examples of using the CDK in Scala (github/cdk/cdk-scala-examples). When I was writing this it sprung to mind that it would be cool to (ab)use one feature for interop... - Egon Willighagen
Egon Willighagen
Programming in the Life Sciences #20: extracting data from JSON I previously wrote about the JavaScript... - https://plus.google.com/1041867...
Programming in the Life Sciences #20: extracting data from JSON I previously wrote about the JavaScript Object Notation (JSON) which has become a de facto standard for sharing data by web services. I personally still prefer something using the Resource Description Framework (RDF) because of its clear link to ontologies,... I previously wrote about the JavaScript Object Notation (JSON) which has become a de facto standard for sharing data by web services. I personally still prefer something using the Resource Description Framework (RDF) because ... - Egon Willighagen
Egon Willighagen
Programming in the Life Sciences #19: debugging Debugging is the process find removing a fault in your... - https://plus.google.com/1041867...
Programming in the Life Sciences #19: debugging Debugging is the process find removing a fault in your code ( the etymology goes further back than the moth story, I learned today). Being able to debug is an essential programming skill, and being able to program flawlessly is not enough; the bug can be ou... Debugging is the process find removing a fault in your code (the etymology goes further back than the moth story, I learned today). Being able to debug is an essential programming skill, and being able to program flawlessly i... - Egon Willighagen
Egon Willighagen
BioScience, Vol. 63, No. 4. (1 April 2013), pp. 245-246, doi:10.1525/bio.2013.63.4.2 Paula Stephan - Egon Willighagen
Egon Willighagen
We are continuing with our weekly releases of highly-requested items from the ORCID iDeas Forum. This post includes the third end-of-the-year goody that we recently released: ORCID iD QR codes. You can now get a scannable QR Code that points to your ORCID iD. In addition, we’ve teamed up with Zazzle.com to format the QR code to be printed on stickers that you can add to your posters and other presentation materials. - Egon Willighagen
Egon Willighagen
Mmm... buffer I don't know yet... - https://plus.google.com/1041867...
Mmm... buffer I don't know yet...  We explore Buffer, Hootsuite, and IFTTT to help academics find the best ways to save time managing their social media accounts. - Egon Willighagen
Egon Willighagen
One hour HTML+ops.js+d3.js hack! I love good libraries! - Egon Willighagen
Egon Willighagen
Honorary degrees will be awarded during the official celebration of the Dies Natalis on 16 January 2015 - Egon Willighagen
Egon Willighagen
Reshared post from PHD Comics: - https://plus.google.com/1041867...
And then people wonder why the retraction rate is going up :) Original Post from PHD Comics: The academic review process. http://www.phdcomics.com/comics... Link to Piled Higher and Deeper - Egon Willighagen
Egon Willighagen
Maastricht railway station - http://en.wikipedia.org/w...
Egonw: {{Infobox station | name = Maastricht | style = NS | image = Maastricht, station.gif | image_caption = | address = | country = [[Netherlands]] | latd = 50|latm = 51|lats = 00 |latNS = N | longd = 5|longm = 42|longs = 19 |longEW = E | iso_region = NL | coordinates_display = yes | line = [[Maastricht–Venlo railway]]<br>[[Maastricht–Aachen railway]]<br>[[Liège–Maastricht railway]] | platform = | opened = 1853 | closed = | code = | services = {{s-rail|title=Nederlandse Spoorwegen}} {{s-line|system=NS Intercity|line=800|branch=800|previous=Sittard|next=}} {{s-line|system=NS Sneltrein|line=32100|previous=|next=Meerssen}} {{s-line|system=NS Stoptrein|line=5300|previous=|next=Maastricht Randwyck}} {{s-line|system=NS Stoptrein|line=6800|previous=Bunde|next=Maastricht Randwyck}} {{s-line|system=NS Stoptrein|line=32000|previous=Maastricht Randwyck|next=Maastricht Noord}} | map_type = Netherlands Dutch railway station | map_caption = }} '''Maastricht''' is a [[railway station]] located in... - Egon Willighagen
Egon Willighagen
Interaction between DNA/histone Methyltransferases and their Inhibitors. - http://www.citeulike.org/user...
Current medicinal chemistry (5 November 2014) Epigenetic research has recently become one of the hotspots in the field of bioscience and drug design. DNA methylation and histone methylation serve a critical function in influencing gene expression and genome function. The inhibition of DNA and histone methyltransferases (DNMTs and HMTs) is a promising approach for the therapeutic treatment of numerous diseases, including cancer. This work reviews the recent achievements in methyltransferase crystallographic structure resolution and bioactive inhibitor screening. We discuss the features of DNA and HMT structures, as well as the mechanism and structure-function relationship of transferase inhibitors, to elucidate how methyltransferase and inhibitor interactions occur both internally and externally. This study briefly reviews the biological function, as well as the inhibitor discovery and development, of DNA/histone methyltransferases. Junchi Hu, Shijie Chen, Xiangqian Kong, Kongkai Zhu,... - Egon Willighagen
Egon Willighagen
What they actually mean:This scientist was a key role in the development of Hollywood. Read her interesting story and learn about her science! Original Post from Fon: This hollywood actress was a key role in the development of WiFi. Read her interesting story and learn why!  This actress from Hollywood's Golden Age reminds us of a time when women were some of the leading unsung tech innovators. - Egon Willighagen
Egon Willighagen
Estimating the intrinsic dimension in fMRI space via dataset fractal analysis - Counting the `cpu cores' of the human brain - http://www.citeulike.org/user...
(27 Oct 2014) Functional Magnetic Resonance Imaging (fMRI) is a powerful non-invasive tool for localizing and analyzing brain activity. This study focuses on one very important aspect of the functional properties of human brain, specifically the estimation of the level of parallelism when performing complex cognitive tasks. Using fMRI as the main modality, the human brain activity is investigated through a purely data-driven signal processing and dimensionality analysis approach. Specifically, the fMRI signal is treated as a multi-dimensional data space and its intrinsic `complexity' is studied via dataset fractal analysis and blind-source separation (BSS) methods. One simulated and two real fMRI datasets are used in combination with Independent Component Analysis (ICA) and fractal analysis for estimating the intrinsic (true) dimensionality, in order to provide data-driven experimental evidence on the number of independent brain processes that run in parallel when visual or... - Egon Willighagen
Cameron Neylon
Does anyone have an up to date figure for subscription market share (by $) of the big trad publishers?
no, sorry. it's a very interesting question. - RepoRat
Generally available in those reports people pay thousands of dollars for...I'm looking at a back of the envelope calculation that gives a jaw dropping result, but I need those figures to confirm... - Cameron Neylon
Ok, not quite so jaw dropping...or maybe...arrgggh...can't get quite the numbers I need to pin this down... - Cameron Neylon
Besides "by $" it would also be interesting to have "by number of pubs" or "by number of journals", because the first I biased towards expensive journals... - Egon Willighagen
Yes, that's kind of my point in this case. Basically I'm trying to calculate how much orgs or countries could do with money saved by subscription cancellations. Often I've got total subscriptions but not by publisher, or by publisher but not the total so I can't calculate proportions... - Cameron Neylon
Yeah, trade secrets... - Egon Willighagen
Egon Willighagen
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data - http://www.citeulike.org/user...
Nucleic Acids Research (27 October 2014), gku1011, doi:10.1093/nar/gku1011 The current version of the Human Disease Ontology (DO) (http://www.disease-ontology.org) database expands the utility of the ontology for the examination and comparison of genetic variation, phenotype, protein, drug and epitope data through the lens of human disease. DO is a biomedical resource of standardized common and rare disease concepts with stable identifiers organized by disease etiology. The content of DO has had 192 revisions since 2012, including the addition of 760 terms. Thirty-two percent of all terms now include definitions. DO has expanded the number and diversity of research communities and community members by 50+ during the past two years. These community members actively submit term requests, coordinate biomedical resource disease representation and provide expert curation guidance. Since the DO 2012 NAR paper, there have been hundreds of term requests and a steady increase in the number of... - Egon Willighagen
Egon Willighagen
See https://github.com/egonw... Fixed the Open PHACTS / d3.js examples. This one showing a pie chart of activity units for all measurements in the ChEMBL data in the cache for paracetamol. - Egon Willighagen
Egon Willighagen
Human Genetics Shape the Gut Microbiome - http://www.citeulike.org/user...
Cell, Vol. 159, No. 4. (7 November 2014), pp. 789-799, doi:10.1016/j.cell.2014.09.053 Host genetics and the gut microbiome can both influence metabolic phenotypes. However, whether host genetic variation shapes the gut microbiome and interacts with it to affect host phenotype is unclear. Here, we compared microbiotas across >1,000 fecal samples obtained from the TwinsUK population, including 416 twin pairs. We identified many microbial taxa whose abundances were influenced by host genetics. The most heritable taxon, the family Christensenellaceae, formed a co-occurrence network with other heritable Bacteria and with methanogenic Archaea. Furthermore, Christensenellaceae and its partners were enriched in individuals with low body mass index (BMI). An obese-associated microbiome was amended with Christensenella minuta, a cultured member of the Christensenellaceae, and transplanted to germ-free mice. C. minuta amendment reduced weight gain and altered the microbiome of recipient mice.... - Egon Willighagen
Egon Willighagen
This MSP “Programming in the Life Science” (PRA3006) student is working with various Open PHACTS API calls. - Egon Willighagen
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