Design and Implementation of a Domain Specific Language for Next Generation Sequence Analysis
Paulo Monteiro,
Departamento de Engenharia Informática –
Abstract:
Next Generation Sequecing (NGS) is a set of molecular biology technologies
which generate, at low cost, many millions of short nucleotide reads. Typical
datasets consist of tens of millions of reads, with each read comprising 35-500
basepairs (depending on the technology used, different read sizes can be
obtained).
There are many tools for handing these datasets. However, they must still be
combined to build a full analysis pipeline. Current solutions to build these
pipelines are Make-like tools which can handle text-files and Unix-like
commands. Several GUI-based solutions allow users who are not comfortable with
the command line to build and run these pipelines. However, they still operate
at the semantic level of Make: file dependencies and transformation commands.
Because each problem and each variation on the technology requires a
different processing pipeline, it would be impossible to design a single
pipeline for every need. This paper aims at the description of a context aware tool
that will allow for the first phase of NGS analysis.
Date: 2014-Feb-06 Time: 14:30:00 Room: 336
For more information:
- http://kdbio.inesc-id.pt/cms/
- lsr@kdbio.inesc-id.pt
- (+351) 21 31 00272
Upcoming Events
INESC Brussels HUB Winter Meeting 2023

This edition of the HUB Winter Meeting will be co-organised with Science Business and will take place on the 30 and 31 January, in Lisbon, at Instituto Superior Técnico, Department of Computer Science and Engineering.
Please see below a summary of the agenda, this will be updated on the INESC Brussels HUB website regularly (confirmed speakers and other relevant info). Places for onsite participation are limited so registration is mandatory. Online participants will be sent a ZOOM link for each specific session on the 27th January.
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9h to 10h30 GMT
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d) Roundtable: From rhetoric to reality – Embedding international strategy in the DNA of research organisations.
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Tuesday, 31 January
f) Workshop: How they did it? Strategic positioning for structural success in Horizon Europe: a discussion of best practices.
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g) The public consultation on European R&I Programmes: Towards FP10.
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h) Networking Lunch (for all onsite participants).
i) Management Committee meeting (Directors and POB members)
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– Discuss key research and innovation issues at EU level.
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