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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
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
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
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
Programming in the Life Sciences #20: extracting data from JSON - http://chem-bla-ics.blogspot.com/2014...
Programming in the Life Sciences #20: extracting data from JSON
Programming in the Life Sciences #19: debugging - http://chem-bla-ics.blogspot.com/2014...
Programming in the Life Sciences #19: debugging
Programming in the Life Sciences #18: Molecular weight distribution of compounds with measured activities against a target (and other examples) - http://chem-bla-ics.blogspot.com/2014...
Programming in the Life Sciences #18: Molecular weight distribution of compounds with measured activities against a target (and other examples)
How to Exploit Postdocs - http://www.citeulike.org/user...
BioScience, Vol. 63, No. 4. (1 April 2013), pp. 245-246, doi:10.1525/bio.2013.63.4.2 Paula Stephan - 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
egonw pushed to master at egonw/mscpils - https://github.com/egonw...
egonw pushed to master at egonw/mscpils
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
One hour HTML+ops.js+d3.js hack! I love good libraries! - http://egonw.tumblr.com/post...
One hour HTML+ops.js+d3.js hack! I love good libraries!
egonw pushed to gh-pages at egonw/mscpils - https://github.com/egonw...
egonw pushed to gh-pages at egonw/mscpils
egonw pushed to master at egonw/mscpils - https://github.com/egonw...
egonw pushed to master at egonw/mscpils
One hour HTML+ops.js+d3.js hack! I love good libraries! - Egon Willighagen
egonw opened issue BiGCAT-UM/bridgedb-r#7 - https://github.com/BiGCAT-...
egonw opened issue BiGCAT-UM/bridgedb-r#7
egonw closed issue egonw/mscpils#2 - https://github.com/egonw...
egonw closed issue egonw/mscpils#2
egonw commented on issue egonw/mscpils#2 - https://github.com/egonw...
egonw commented on issue egonw/mscpils#2
egonw pushed to gh-pages at egonw/mscpils - https://github.com/egonw...
egonw pushed to gh-pages at egonw/mscpils
egonw pushed to gh-pages at egonw/mscpils - https://github.com/egonw...
egonw pushed to gh-pages at egonw/mscpils
egonw pushed to gh-pages at egonw/mscpils - https://github.com/egonw...
egonw pushed to gh-pages at egonw/mscpils
egonw created branch gh-pages at egonw/mscpils - https://github.com/egonw...
egonw created branch gh-pages at egonw/mscpils
egonw pushed to master at egonw/mscpils - https://github.com/egonw...
egonw pushed to master at egonw/mscpils
Honorary degrees will be awarded during the official celebration of the Dies Natalis on 16 January 2015 - Egon Willighagen
egonw opened issue egonw/mscpils#2 - https://github.com/egonw...
egonw opened issue egonw/mscpils#2
egonw opened issue egonw/mscpils#1 - https://github.com/egonw...
egonw opened issue egonw/mscpils#1
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
egonw opened pull request openphacts/ops.js#6 - https://github.com/openpha...
egonw opened pull request openphacts/ops.js#6
egonw created branch feature-1.4/datasources at egonw/ops.js - https://github.com/egonw...
egonw created branch feature-1.4/datasources at egonw/ops.js
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
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