Workshop on
NCBI, Pubmed & other open source software
11 – 13 April 2016
Draft vs 160104
Introduction
The National Center for Biotechnology Information (NCBI) is used daily by most life
scientists, to search for literature, align nucleotides or proteins sequences, or obtain
detailed information on specific nucleotides and proteins.
This short course will cover these better-known-uses of NCBI with additional attention
given to exploring other tools and databases aggregated at NCBI, as well as
maximising the potential of the free-to-access Pubmed. The last day will be a
bioinformatics course specifically aimed at bench scientists with little Bioinformatics
experience. This part will focus on 'hacking' excel, which together with other free, easyto-use tools can be used to quickly interrogate 'omics' results across virtually any publicly
accessible database.
This course is organized by the Bioinformatics Dept. of the Erasmus MC and the
Postgraduate School Molecular Medicine.
Program
The program features several short, concentrated presentations on various aspects of the
data analysis, followed by interactive practical sessions behind the computers.
Location:
Duration:
Participants:
Dept. of Bioinformatics, computer room, Ee 15.28
(15th floor), Erasmus MC
9.30 – 16.30 (including lunch break and coffee breaks)
Max. 18 participants
Summary
Day 1 and 2: NCBI: a bag of mixed lollies for life scientists.
This part will start with an overview of NCBI and will cover as well:
1. GEO (Gene Expression Omnibus)
- uploading data
- downloading data (via GUI and BioConductor's geo2r() function)
- NCBI analysis of GEO stored data
2. Sequence alignment (nucleotide and peptide)
3. Annotation (genes and proteins)
Day 1 and 2: Systematic Literature Retrieval (in PubMed)
The focus of these workshops will be on the systematicity of creating a search strategy,
and not too much on PubMed. How do you know you did not miss important papers.
PubMed is the most used database for medical literature searching, but many people use
it suboptimal. PubMed is not a medical Google. We can teach you how to make PubMed a
more valuable tool for day-to-day searches and the important searches for systematic
reviews and theses, and while doing so can warn you about some hidden pitfalls of
PubMed.
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Day 3: Search and Integration strategies for gene and drug target information
This workshop will detail how to select good keywords for searching gene and drug target
information, and how to generate with minimum effort a simple data file to gain direct
access to many gene information web sites for many genes.
Detailed program
Monday, 11 April 2016
NCBI, Pubmed
Time
Speakers
Title
Keywords
09.30–10.45
Andrew Stubbs
NCBI: a bag of mixed
lollies for life scientists
11.00–12.30
Andrew Stubbs
Gene Expression
Omnibus (GEO )
GEO; Sequence
alignment; Annotation
(genes and proteins),
clinical variation,
genome browser
GEO practical
12.30–13.15
13.15–16.15
Lunch
Wichor Bramer
Systematic Literature
Retrieval
Pubmed
Tuesday, 12 April 2016
NCBI, Pubmed
Time
Speakers
Title
Keywords
09.30–12.30
Wichor Bramer
Systematic Literature
Retrieval (cont.’d)
NCBI: a bag of mixed
lollies for life scientists
(cont.’d)
Pubmed
Clinical variation
resources
Clinical variation
resources
Clinvar, dbSNP, dbGap,
Genome view
Practical: Clinvar,
dbSNP, dbGap, Genome
view
Karl Brand, Justine Peeters,
and Mario Pescatori
12.30–13.15
13.15–14.15
Lunch
Andrew Stubbs
14.15–16.15
Andrew Stubbs, David van
Zessen
GEO; Sequence
alignment; Annotation
(genes and proteins)
Wednesday, 13 April 2016
NCBI blast and other public domain software and applications
Time
Speakers
Title
Keywords
09.30–10.45
Jean-Marc Neefs
11.00–12.30
Blast (SRA blast), BLAT,
others?
Practical: Blast (SRA
blast), BLAT, others?
12.30–13.15
13.15–14.15
14.15–16.15
Jean-Marc Neefs and
Andrew Stubbs
Lunch
Jean-Marc Neefs
Jean-Marc Neefs
Sequence analysis
strategies
Sequence analysis
strategies
16.15–16.30
Andrew Stubbs
Information retrieval
Integrative analysis and
reporting – A
programming free
environment
Course Summary
Sources and pitfalls
Practical: Integrative
analysis
No programming
required
Take home message
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Attendance fees
The subscription fee of non-commercial participants for the Course is € 500.
Discounts are handled as followed:
- PhD students get a discount of 50% and pay €250.
- Only participants from the postgraduate school MolMed and members of the Bio
Informatics Dept. get a discount of 100% and pay €0.
- MGC members and master students from elsewhere get a discount of 50% and pay
€250.
Master students from elsewhere who pay the fee from their personal budget get a discount of 75%
and pay €125.
Invoices
Fees can be paid upon an INVOICE. Shortly after your registration you will receive the
INVOICE per mail. Payment per bank can be done on account: 43.47.01.408 / Erasmus
MC, (IBAN code bank: NL86ANBA0434701408; SWIFT code bank: ABNANL2A), together
with the number on your INVOICE. Late participants can also pay in cash upon signing in
for the Course.
Cancellations
Our cancellation policy is that cancellation is possible up to one week before the start of
the Course. Later cancellation will not be accepted, but you are allowed to send a
substitute.
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