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Node: Italy 

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Target audience: PhD Students or young resea...  or Bioinformatics beginners  

  • Training course on Python for Life Scientists

    11 - 15 September 2017

    Roma, Italy

    Training course on Python for Life Scientists https://tess.elixir-europe.org/events/training-course-on-python-for-life-scientists Python is an object-oriented programming language that is ideal for biological data analysis. The course will start from zero knowledge, and will introduce the participants to all the basic concepts of Python such as calculating, organizing data, reading and writing files, program logic and writing larger programs. All the examples and practical sessions will focus on solving biological problems. In particular the sessions will cover: - working with DNA and protein sequences - data retrieval from files and their manipulation - running applications, such as BLAST, locally and from a script - finding motifs in sequence - parsing common file formats (Uniprot, GenBank, PDB) - ways to find and correct program errors. The course will be highly interactive and the students will continuously put theory into practice while learning. Basic Unix/Linux skills will be provided at the beginning of the course. 2017-09-11 09:00:00 UTC 2017-09-15 18:00:00 UTC Veronica Morea (CNR-IBPM, Rome, Italy), Allegra Via (ELIXIR-IIB Training Coordinator, CNR-IBPM, Italy), Loredana Le Pera (ELIXIR-IIB Training Team, IIT@Sapienza, Italy) Dipartimento di Scienze Biochimiche - Alessandro Rossi Fanelli, 332, Viale Regina Elena, Roma, Italy Dipartimento di Scienze Biochimiche - Alessandro Rossi Fanelli, 332, Viale Regina Elena Roma Città Metropolitana di Roma Italy 00185 Computer science Bioinformatics Computational biology Sapienza University of Rome elixir.ita.training@gmail.com, loredanalepera@gmail.com ELIXIR Italy BiologistsBioinformatics beginners 20 workshops_and_courses first_come_first_servedregistration_of_interest Python for BiologistsbioinformaticsComputer ProgrammingBiological databasesPython
  • Linux shell scripting for high-throughput biological data processing on supercomputers

    16 - 17 January 2018

    Roma, Italy

    Linux shell scripting for high-throughput biological data processing on supercomputers https://tess.elixir-europe.org/events/linux-shell-scripting-for-high-throughput-biological-data-processing-on-supercomputers An unprecedented amount of biomedical data have been produced and stored in the last years. Managing such biological big data is often not affordable without high-performance computing architectures, needed to analyze and process large-scale datasets. Running high-throughput (HTP) bioinformatics data pipelines on supercomputing machines requires advanced Linux shell command line and scripting skills. Most scientists working with such data often lack such skills or have acquired them by self-learning without becoming fully independent and fluent. This may have repercussions on the quality, reproducibility, and reliability of the analyses. In this two-day course, we will introduce the Linux shell and, on day one, we will show how to navigate and work with files and directories, how to combine commands to do new things, how to perform the same actions on many different files, how to filter and selectively extract data from tables, and how to find objects in files. Moreover, we will show how to connect to a remote supercomputer and how to utilise a supercomputing environment to analyse big amount of biological data, run simple shell scripts and bioinformatics pipelines. Day 2 will be wholly practical. Participants are invited to let us know in advance which are the typical file format(s) they have to deal with (e.g. fastq, table, etc), the typical processes they need to perform on them (e.g. filtering, ordering, etc.) and the typical programs they need to run (e.g. bwa, hisat2, etc.) so that we can prepare tailored practicals. Participants are also welcome to come to the course with one or more files they wish to work with, provided they do not exceed a given size. 2018-01-16 09:00:00 UTC 2018-01-17 18:00:00 UTC Allegra Via (ELIXIR-IIB Training Coordinator, IBPM-CNR, IT) Loredana Le Pera (ELIXIR-IIB Training Team, IBIOM-CNR, IT) Tiziana Castrignanò (SCAI Department, CINECA, Roma, IT) Via dei Tizii, 6B, Roma, Italy Via dei Tizii, 6B Roma Città Metropolitana di Roma Italy 00185 Data mining Bioinformatics CINECA elixir.ita.training@gmail.com [] Biologistsbeginner bioinformaticiansBiomedical researchersPhD Students or young researchers in molecular biology and/or genetics with little or no background in bioinformatics. 20 workshops_and_courses first_come_first_servedregistration_of_interest Unix/LinuxHTP dataShell scriptManaging and Processing datasupercomputer

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