Parsing for bioinformatics in Perl 6

Overview

Parsing is the process of detecting and verifying the structure of incoming data and then processing that data so as to make it available to a program in convenient ways.

This full-day tutorial will introduce beginner and intermediate programmers to the powerful and efficient parsing mechanisms built into Perl 6, and will explore specific techniques for parsing data in a variety of commonly used formats. Most examples will be based on typical parsing problems encountered in Bioinformatics.

Topics covered include:

• simple parsing with regexes

• structured parsing with grammars

• processing comma-separated text

• dealing with XML and other tagged formats

• decoding heterogeneous structured formats such as FASTA, Swiss-Prot, GenBank, and BLAST reports

• handling queries in synthetic and natural languages

• extracting data structures from structured data

• processing file inclusions

• coping with incomplete, malformed, and ambiguous data

• selecting and using appropriate parsing tools from the CPAN

• integrating parsing and object oriented programming

• data mining (parsing as a data recognition tool)

• error detection and consistency checking (parsing as a data validation tool)

• structured I/O (parsing as a data acquisition tool)

• recognition and extraction (parsing as a data search tool)

• hierarchical data processing (parsing as a data transformation tool)

• task specific languages (parsing as a command specification tool)

This class is taught by Damian Conway, a well-known speaker and lecturer (see his official biography or his Wikipedia page). Damian already lectured at SIB several times, and consistently received amazing feedback about his courses.

Audience

Anyone who has to do programming in bioinformatics (not necessarily in Perl), and is interested to know about new tools.

Prerequisites

Some knowledge in programming (any language).

Application

The cost of this workshop is subsidised by the SIB Swiss Institute of Bioinformatics; the registration fee is only 20 CHF and cover the printing of course material. Participants registering with a SIB email address can attend the workshop for free, but they need to register.

Deadline for registration and free-of-charge cancellation is set to 24 April. Participants who cancel after this date will not be reimbursed. Please note that participation to SIB courses is subject to this and other general conditions, available at https://www.sib.swiss/training/terms-and-conditions

You will be informed by email of your registration confirmation.

Location

University of Lausanne

Additional information

Coordination: Frédéric Schütz, Training group at SIB

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Please contact training@sib.swiss if you have any question.