Workshop NCBI, Pubmed & other open source software

Course date: 04 June 2018 - 06 June 2018
Location: Erasmus MC, Ee-15.28

Click here for details of programme
Click here to register for this course
Click here for abstracts/reviews in preparation of the course


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. Apart from that, 3 speakers will give a short presentation about their own experiences with the use of publicly available research data from the web at the end of each day.

This course is organized by the Bioinformatics Dept. of the Erasmus MC and 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.

Location:                          Dept. of Bioinformatics, computer room, Ee 15.28
(15th floor), Erasmus MC
Duration:                         9.30 – 17.00 (including lunch break and coffee breaks) 

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.NCBI reference databases (e.g. RefSeq, HGVS, Clinvar, Sequence Read Archive)
2.Annotation (genes and proteins)
3.Gene expression analysis : GEO (Gene Expression Omnibus) and GEO2R (BioConductor's function)
4.Sequence alignment (nucleotide and peptide): BLAST (including Genome BLAST)
5.NGS analysis: Genome workbench (desktop BAM analysis), Clinvar & Variation Viewer

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

Attendance fees

The subscription fee of non-commercial participants for the Course is € 600.

Discounts are handled as followed: 

- PhD students get a discount of 50% and pay €300.

- 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 €300.

Master students from elsewhere who pay the fee from their personal budget get a discount of 75% and pay €125. If these financial requirements pose a problem but you wish to attend the Course and Workshops, please contact Frank van Vliet, managing director of the Erasmus Postgraduate School Mol Med, at: 


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: NL86ABNA0434701408; 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.

General information

Financial regulation of the Postgraduate School MolMed

From January 1st, 2017 the following financial rules apply, but they may differ per course still. Look at the course fee of each course to be sure which discounts are really applied:

Non-commercial course, symposium or workshop fee: €200/day, €750/week

• Participants of the postgraduate school MolMed: discount of 100%

• However, the Research Management course and the workshops Photoshop/Illustrator/Indesign have to be paid from the ‘personal budget’ of employees, MolMed members and PhD students included. So they will receive an invoice from us which you have to pay and which will be reimbursed by your Department. When you will pay from your personal budget you need to provide us your home address details for the invoice

• PhD students and Master’s students, regardless of institution: discount of 50%.

•The course fees of research master’s students will be paid by their master program at rate of €100/ECTS. For not I&I master students: please inform your master program in advance whether they agree to pay.

•Master’s students who are paying the fee from their private budget: discount of 75%. When you will pay from your personal budget you need to provide us your home address details for the invoice.

•However, 2 courses in statistics are paid centrally by the Dept. of Research policy for all PhD students from Erasmus MC! These are R and the SPSS course. So for Erasmus MC PhD students, these courses are always free, provided you are officially registered as a PhD student.

There is one fee for the entire course. There is no reduction for partial participation.
Some courses have less course days: SPSS 3 days, Survival Analysis 2 days, Management 2 days, Presenting 1,5 days and also other may be shorter as indicated on the website.Commercial participants, companies & sponsors are invited to inquire about commercial tuition fees and about sponsoring.

All invoices will be sent by email to the mail address that you filled in upon registration. If this address is not correct we use your Erasmus MC address.

Those who register for a course, symposium or workshop agree with these financial conditions.

Click here for details of programme
Click here for Abstracts/reviews in preparation of the course (available soon!)
Click here to register for this course

Click here for the other items