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  • Introduction to Regular Expressions

    18 March 2020

    Heidelberg, Germany

    Introduction to Regular Expressions Educators: Supriya Khedkar, Toby Hodges (HD-HuB) Date: 18/03/2020 09:30 - 16:00 Location: EMBL Heidelberg; Room 202 Contents: Do you often work with lots of data files on the computer, are you often trying to spot particular files or lines of text in them that are important for you? If so, then using regular expressions could save you a lot of time and frustration! Regular expressions (regex/REs) are a language designed to describe patterns of characters that you want to match in a body of text. For example, if you want to extract every Ensembl Gene ID in a GFF file, find tandem repeats in a large set of sequences, or extract every email address in a large document, regular expressions are the perfect tool. Regular expressions are incorporated into a wide range of software and programming languages, and the workshop will include examples of their use on the UNIX command line and in R and Python. Learning goals: This workshop will provide an introduction to REs and cover some of the simple but powerful ways that these can be used to find patterns in large volumes of text data. The workshop will be interactive and driven by examples to demonstrate how you might use regular expressions in your work. Prerequisites: Participants are required to bring their own laptop to the workshop, with a text editor suitable for programming (e.g. Atom, Sublime Text, VSCode, Notepad++) installed. Keywords: UNIX command line, R, Python Tools: UNIX command line, R, Python 2020-03-18 09:00:00 UTC 2020-03-18 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • Proteomics and Metabolomics with OpenMS

    27 - 29 April 2020

    Boston, United States of America

    Proteomics and Metabolomics with OpenMS Educators: Oliver Kohlbacher, Julianus Pfeuffer, Timo Sachsenberg (CIBI), assisted by Oliver Alka Date: April 27 - April 29 Location: Northeastern University 315 and 320 Shillman Hall 115 Forsyth Street, Boston, Massachusetts 02115, USA Keynote Speakers: Oliver Kohlbacher Contents: The course introduces key concepts of non-targeted label-free proteomics and metabolomics. Non-targeted methods are ideal for unbiased discovery studies and scale well for large-scale studies (e.g., clinical proteomics/metabolomics). Based on example datasets we will then introduce several open-source software tools for proteomics and metabolomics, primarily focusing on OpenMS ( We will demonstrate how these tools can be combined into complex data analysis workflows including visualization of results. Participants will have the opportunity to bring their own data and design custom analysis workflows together with instructors. Target audience: Target audience are experimental scientists with experience in proteomic and/or metabolomic research. We also welcome computational scientists interested in working with raw mass spectrometric data. Software Requirements: The participants should bring their own laptop computers. Instructions regarding downloading and installing all required software (Windows, OSX, or Linux) will be provided prior to the course. Installer versions of all required software will be available. Keywords: LC-MS based proteomics and metabolomics, OpenMS, workflows, KNIME, data analysis Tools: OpenMS, KNIME 2020-04-27 09:00:00 UTC 2020-04-29 17:00:00 UTC de.NBI Boston, Boston, United States of America Boston Boston Suffolk County United States of America [] [] [] workshops_and_courses [] []
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