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Egon Willighagen › Comments

Egon Willighagen
(2004) "Metabolism at a Glance will be an essential resource for students in medical, biochemistry, veterinary, sports science and nutrition courses requiring a knowledge of intermediary metabolism. Those who need an authoritative yet concise guide to metabolism, such as examination candidates, biomedical scientists, and clinicians specialising in diabetes as well as inborn errors of metabolism, will find this book invaluable. The book is designed to fit into the reading time as well as the budget of students and trainees and has established itself as an enormously popular book amongst students and lecturers alike."--Jacket. JG Salway - Egon Willighagen
Egon Willighagen
Implementing Transitive Credit with JSON-LD - http://www.citeulike.org/user...
(2 Sep 2014) Science and engineering research increasingly relies on activities that facilitate research but are not currently rewarded or recognized, such as: data sharing; developing common data resources, software and methodologies; and annotating data and publications. To promote and advance these activities, we must develop mechanisms for assigning credit, facilitate the appropriate attribution of research outcomes, devise incentives for activities that facilitate research, and allocate funds to maximize return on investment. In this article, we focus on addressing the issue of assigning credit for both direct and indirect contributions, specifically by using JSON-LD to implement a prototype transitive credit system. Daniel Katz, Arfon Smith - Egon Willighagen
Egon Willighagen
Including "Implementing Transitive Credit with JSON-LD" [0] for ctiation credit for papers citing software... - https://plus.google.com/1041867...
Including "Implementing Transitive Credit with JSON-LD" [0] for ctiation credit for papers citing software that cites papers, etc... haven't read it yet, but hopefully extends CiTO [1]. 0. http://arxiv.org/abs/1407.5117 1. http://www.jbiomedsem.com/content... A talk about why metrics and citation for software (and data) are important to NSF and the science & engineering community, and what a number of projects are trying to do to improve the situation. Presented at "Workshop on Supporting Scientific Discovery through Norms and Practices for Software and Data Citation and Attribution", Washington, DC, 29 Jan 2015 - Egon Willighagen
Egon Willighagen
De mooie voedselmachine : alles over de darmen, een onderschat orgaan - http://www.citeulike.org/user...
(2014) Giulia Enders, Jill Enders, Jolanda Lindert - Egon Willighagen
Egon Willighagen
The official source for information about Google Scholar - Egon Willighagen
Egon Willighagen
LaTeX, Git, and online collaboration... - https://plus.google.com/1041867...
LaTeX, Git, and online collaboration... One of your most requested features - a link between Overleaf and Git - is now available in beta release - Egon Willighagen
Egon Willighagen
Mmm... that means that the file readers from the Chemistry Development Kit should have gained some speeds... - https://plus.google.com/1041867...
Mmm... that means that the file readers from the Chemistry Development Kit should have gained some speeds with the newer Java VMs! Here substring was used on lines to get things like the chemical element symbol... If I understand correctly, would the reader keep some information from each line, it had kept the whole file in memory until the read molecule was deleted! :( HT +NextMove Software  The substring() method is one of most used methods for String manipulation in any language. Which is why thesubstring() in java is highly optimized for the cases where we are generating a lot of su... - Egon Willighagen
Egon Willighagen
The journal club can represent a major intellectual investment – and a long-standing form of post-publication evaluation. We’re launching a new initiative to encourage journal clubs to share their ... - Egon Willighagen
Egon Willighagen
Coulomb explosion during the early stages of the reaction of alkali metals with water - http://www.citeulike.org/user...
Nature Chemistry (26 January 2015), doi:10.1038/nchem.2161 Philip Mason, Frank Uhlig, Václav Vaněk, Tillmann Buttersack, Sigurd Bauerecker, Pavel Jungwirth - Egon Willighagen
Egon Willighagen
#CoulombExplosion Als je natrium of kalium in water gooit, ontploft in eerste instantie het metaal zélf. De gevormde waterstof knalt pas later, melden Tsjechische onderzoekers in Nature Chemistry . - Egon Willighagen
Egon Willighagen
References in #wikidata  How to add a CAS registry number and how to show where you got the information... - https://plus.google.com/1041867...
References in #wikidata  How to add a CAS registry number and how to show where you got the information. Provenance in Wikidata about a statement that diamond has a particular CAS registry number. Now I wonder if it even lists that I added that reference… Provenance all the way down? - Egon Willighagen
Egon Willighagen
Automated Lead Optimization of MMP-12 Inhibitors Using a Genetic Algorithm - http://www.citeulike.org/user...
ACS Med. Chem. Lett. In ACS Medicinal Chemistry Letters, Vol. 2, No. 1. (20 October 2010), pp. 28-33, doi:10.1021/ml100191f Traditional lead optimization projects involve long synthesis and testing cycles, favoring extensive structure?activity relationship (SAR) analysis and molecular design steps, in an attempt to limit the number of cycles that a project must run to optimize a development candidate. Microfluidic-based chemistry and biology platforms, with cycle times of minutes rather than weeks, lend themselves to unattended autonomous operation. The bottleneck in the lead optimization process is therefore shifted from synthesis or test to SAR analysis and design. As such, the way is open to an algorithm-directed process, without the need for detailed user data analysis. Here, we present results of two synthesis and screening experiments, undertaken using traditional methodology, to validate a genetic algorithm optimization process for future application to a microfluidic system.... - Egon Willighagen
Egon Willighagen
Use-Dependent Cortical Processing from Fingertips in Touchscreen Phone Users - http://www.citeulike.org/user...
Current Biology, Vol. 25, No. 1. (26 January 2015), pp. 109-116, doi:10.1016/j.cub.2014.11.026 Cortical activity allotted to the tactile receptors on fingertips conforms to skilful use of the hand [1?3]. For instance, in string instrument players, the somatosensory cortical activity in response to touch on the little fingertip is larger than that in control subjects [1]. Such plasticity of the fingertip sensory representation is not limited to extraordinary skills and occurs in monkeys trained to repetitively grasp and release a handle as well [4]. Touchscreen phones also require repetitive finger movements, but whether and how the cortex conforms to this is unknown. By using electroencephalography (EEG), we measured the cortical potentials in response to mechanical touch on the thumb, index, and middle fingertips of touchscreen phone users and nonusers (owning only old-technology mobile phones). Although the thumb interacted predominantly with the screen, the potentials associated... - Egon Willighagen
Egon Willighagen
Reshared post from NextMove Software: - https://plus.google.com/1041867...
Now, had they not had access to the data... (enter my PhD time....)... Original Post from NextMove Software: What is the best way of laying out the rows and columns of an NxN 2D activity matrix, in order to identify gaps worth pursuing? There is a nice dataset in the supporting information for Pickett et al. that illustrates how the sort order of rows and columns in an activity heatmap can hinder/help the identification of gaps which should be filled. First of all, here is the heatmap in question, a 50×50 array. - Egon Willighagen
Egon Willighagen
Optimization of Distributed SPARQL Queries Using Edmonds' Algorithm and Prim's Algorithm - http://www.citeulike.org/user...
In Computational Science and Engineering, 2009. CSE '09. International Conference on, Vol. 1 (August 2009), pp. 330-337, doi:10.1109/cse.2009.144 BP Vandervalk, EL McCarthy, MD Wilkinson - Egon Willighagen
Egon Willighagen
The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions - http://www.citeulike.org/user...
JMIR Research Protocols, Vol. 2, No. 1. (05 April 2013), e14, doi:10.2196/resprot.2315 Ben Vandervalk, Luke McCarthy, José Cruz-Toledo, Artjom Klein, Christopher Baker, Michel Dumontier, Mark Wilkinson - Egon Willighagen
Egon Willighagen
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains - http://www.citeulike.org/user...
Journal of Biomedical Semantics, Vol. 5, No. 1. (2014), 5, doi:10.1186/2041-1480-5-5 The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these... - Egon Willighagen
Egon Willighagen
Original Post from Ambit: AMBIT Web services 2.7.2 release  - UI for Read across workflow - Database and REST API support for Read across assessments - Various dependencies updated - Improved API-DOCS http://ideaconsult.github.io/example... - Improved SMIRKS parser - Bug fixes See http://ambit.sf.net for download, installation and user guides. AMBIT - Egon Willighagen
Egon Willighagen
Influence of melatonin receptor signalling on parameters involved in blood glucose regulation - http://www.citeulike.org/user...
Journal of Pineal Research, Vol. 56, No. 1. (January 2014), pp. 82-96, doi:10.1111/jpi.12100 Ivonne Bazwinsky-Wutschke, Lars Bieseke, Eckhard Mühlbauer, Elmar Peschke - Egon Willighagen
Egon Willighagen
An introduction to systems toxicology - http://www.citeulike.org/user...
Toxicol. Res., Vol. 4, No. 1. (2015), pp. 9-22, doi:10.1039/c4tx00058g The science of toxicology is the science of the system. Toxicologists aim to understand and predict the adverse effects of chemicals on biological systems. As biological systems are extremely complex, the challenge of predicting human toxicity early in the drug discovery process is immense. In the past decades, a huge effort has been undertaken to characterise the impact of chemicals on biological systems using in vitro, pre-clinical and clinical approaches. This has led to a vast amount of knowledge on the biology of systems, especially as a result of the data deluge from -omic level investigations. However, a lack of robust and comprehensive integration has meant that this wealth of data has still not led to accurate prediction of toxicity in a single system, or the ability to extrapolate robustly between systems. The new discipline of systems toxicology aims to take the computational approaches developed in... - Egon Willighagen
Egon Willighagen
With WAPT, IT teams can manage simply and effectively the lifecycle of an installed base of Windows applications. WAPT can (1) install, (2) update, (3) configure, (4) uninstall and (5) inventory your Windows based applications, be they business, office, utilities or even system drivers. - Egon Willighagen
Egon Willighagen
Reshared post from Andrew Su: - https://plus.google.com/1041867...
Oh, wow! Great software! Where can I download the source code? Original Post from Andrew Su: Lazy Saturday? Try our #citizenscience app to advance biomedical research http://mark2cure.org/beta. If you can read, you can help! Mark2Cure - Egon Willighagen
Egon Willighagen
Rational design of functional and tunable oscillating enzymatic networks - http://www.citeulike.org/user...
Nature Chemistry, Vol. 7, No. 2. (12 January 2015), pp. 160-165, doi:10.1038/nchem.2142 Sergey Semenov, Albert Wong, Martijn van der Made, Sjoerd Postma, Joost Groen, Hendrik van Roekel, Tom de Greef, Wilhelm Huck - Egon Willighagen
Egon Willighagen
“Nice thread: https://t.co/OeRSSOHu24 Using @neo4j for @wikidata and #DBpedia with @kennybastani and @danbri” - Egon Willighagen
Egon Willighagen
A single pair of neurons links sleep to memory consolidation in Drosophila melanogaster - http://www.citeulike.org/user...
eLife (07 January 2015), e03868, doi:10.7554/elife.03868 eLife - Open access to the most promising advances in science Paula Haynes, Bethany Christmann, Leslie Griffith, Graeme Davis - Egon Willighagen
Egon Willighagen
Reshared post from Altmetric: - https://plus.google.com/1041867...
Original Post from Altmetric: Who talks about which research? A recent Scientific American visualization examines the differences in what is picked up on by academics vs. the public:  Twitter, mainstream media and academic blogs focus on surprisingly different scientific subjects - Egon Willighagen
Egon Willighagen
Reshared post from Wikidata: - https://plus.google.com/1041867...
Original Post from Wikidata: Want to help out with mapping schema.org and Wikidata properties? Here is the ticket for it: Schema.org should have mappings to Wikidata terms where possible · Issue #280 · schemaorg/schemaorg · GitHub - Egon Willighagen
Egon Willighagen
Time management: Seize the moment - http://www.citeulike.org/user...
Nature, Vol. 517, No. 7535. (21 January 2015), pp. 517-519, doi:10.1038/nj7535-517a Jeffrey Perkel - Egon Willighagen
Egon Willighagen
No paradox, no progress: inverse cancer comorbidity in people with other complex diseases - http://www.citeulike.org/user...
The Lancet Oncology, Vol. 12, No. 6. (June 2011), pp. 604-608, doi:10.1016/s1470-2045(11)70041-9 In the past 5 years, several leading groups have attempted to explain why individuals with Down's syndrome have a reduced risk of many solid tumours and an increased risk of leukaemia and testicular cancer. Niels Bohr, the Danish physicist, noted that a paradox could initiate progress. We think that the paradox of a medical disorder protecting against cancer could be formalised in a new model of inverse cancer morbidity in people with other serious diseases. In this Personal View, we review evidence from epidemiological and clinical studies that supports a consistently lower than expected occurrence of cancer in patients with Down's syndrome, Parkinson's disease, schizophrenia, diabetes, Alzheimer's disease, multiple sclerosis, and anorexia nervosa. Intriguingly, most comorbidities are neuropsychiatric or CNS disorders. We provide a brief overview of evidence indicating genetic and... - Egon Willighagen
Egon Willighagen
eXamine: Exploring annotated modules in networks - http://www.citeulike.org/user...
BMC Bioinformatics, Vol. 15, No. 1. (07 July 2014), 201, doi:10.1186/1471-2105-15-201 Biological networks have a growing importance for the interpretation of high-throughput “omics” data. Integrative network analysis makes use of statistical and combinatorial methods to extract smaller subnetwork modules, and performs enrichment analysis to annotate the modules with ontology terms or other available knowledge. This process results in an annotated module, which retains the original network structure and includes enrichment information as a set system. A major bottleneck is a lack of tools that allow exploring both network structure of extracted modules and its annotations. Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine Smit, Michel Westenberg, Gunnar Klau - Egon Willighagen
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