Workshop on NCBI & other open source software

Course date: 12 May 2014 - 14 May 2014
Location: Erasmus MC, Ee 15.28

Click here for details of programme


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, easy-to-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 together with the Postgraduate School Molecular Medicine.


The program features several short, concentrated presentations on various aspects of the data analysis, followed by interactive practical sessions behind the computers.
The course will be hel at te dept. of Bioinformatics, computer room, Ee 15.28 (15th floor), Erasmus MC.
There is a maximum of 18 participants, due to the number of computers.


Program 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

    - uploading data

    - downloading data (via gui and BioConducotr'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.

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.


Course program - see attached program for all details

1st day: public domain software applications/ NCBI
Morning: Justine Peeters, Andrew Stubbs and Mario Pescatori: databases and connections with R
Afternoon: Wichor Bramer: Pubmed applications (1)
2nd day: NCBI Cont’d
Morning: Wichor Bramer: Pubmed, etc. (2) 
Afternoon: Justine Peeters, Andrew Stubbs, Mario Pescatori
3rd day: other public domain software and applications by Jean Marc Neefs, Johnson & Johnson
basic: excel, Notepad++ and Waverider; gene expression data analysis in clinical trials for monitoring molecular response to drug dosage; or broad: strategies for identification of chemical compounds, drug targets, pharmacological activities, and biological pathways in cancer.
State-of-the-art fragment mapping tools  in next-generation-sequencing; or wide: the current arsenal of tools and databases in computational biology

Full participation in 1,0 ETCS.

Attendance fees
The subscription fee of non-commercial participants for the Course is € 350.
Discounts are handled as followed: 

- PhD students get a discount of 50% and pay €175.
- Only participants from the postgraduate school MolMed get a discount of 100% and pay €0.
- Other Erasmus MC participants, like Nihes and MGC members and master students from elsewhere get a discount of 50% and pay €175.
Master students from elsewhere who pay the fee from their personal budget get a discount of 75% and pay €87,50.
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: / 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.

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.

Click here for details of programme

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