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chem-bla-ics

chem-bla-ics
Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.
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PublishingSmilesAcsChemieEnglisch
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Elsevier is not the only publisher with a large innovation inertia. In fact, I think many large organizations do, particularly if there are too many interdependencies, causing too long lines. Greg Laundrum made me aware that one American Chemical Society journal is now going to encourage (not require) machine readable forms of chemical structures to be included in their flagship. The reasoning by Gilson et al. is balanced.

PublishingTextminingChemieEnglisch
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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 even help forward science, despite crippling progress. That sound harsh, and surely they have done a lot of good for science. In fact, we would not be where we are now without the publishers.

NanosafetyEnanomapperOpentoxOntologyChemieEnglisch
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I am happy that I got my first research grant awarded (EU FP7), which should start after all the contracts are signed, etc, somewhere early 2014. The project is about setting up data needs for the analysis of nanosafety studies. And for this, I have the below two position vacancies available now.

Pra3006HtmlChemieEnglisch
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HTML (HyperText Markup Language), the language of the web, is no longer the only language of the web. But it still is the primary language in which source code of webpages is shared. Originally, HTML pages were always static: the only HTML source of a web page was that was downloaded from a website. Nowadays, much HTML the is visualized in your web browser, is generated on the fly with JavaScript.

Pra3006ChemieEnglisch
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Continuing on the theory covered in this course, this part will talk about application programming interfaces (APIs) and web services. Application Programming Interfaces APIs define how programs can be used by other programs. An API defines how methods are called and what feedback you can expect. It basically is the combination of documentation and the program itself.

Pra3006JavascriptHtmlChemieEnglisch
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One key feature of programming languages is the following: first, there is linearity. This is an important point that is not always clear to students who just start to program. In fact, ask yourself what the algorithm is for counting the chairs in the room where you are now sitting. Could a computer do that in the same way? How should your algorithm change? A key point is, is that the program is run step by step, in a linear way.

Pra3006ChemieEnglisch
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Now that I have wrote out the goals, what they students will practically do, and how to get started with the Open PHACTS platform, I will list how we will assess the students: a presentation on the second day, outlining the project and work plan, working source code at the end of the cour se, a final presentation, showing the results and conclusions. Primarily, they will be judged on their acquired programming skills.

Pra3006JavascriptHtmlOpenphactsChemieEnglisch
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The purpose of a web service is that you give it a question or task, and that it returns an answer. For example, we can ask the Open PHACTS platform what compounds it knows with aspirin in the name. We pass the question (with the API key) and get a list of matching compounds. Now, this communication is complex: it happens at many levels, which are spelled out in the Internet Model.