Online tutorial
EMBL-EBI, programmatically
Take a REST from manual searches
From BLAST searches to literature services, gene annotation and information on protein structure and function, large amounts of biological data can be accessed online with the click of a button. When it comes to repeated tasks with large volumes of data, the best way to get quick and automated access is to do it programmatically.
Who is this course for?
This course consists of a series of recorded webinars as well as documentation, example scripts and live examples. You do not need to watch all of the webinars; you can dip in and out and watch only the webinars you are interested in.
For the introductory webinar all you need is an undergraduate understanding of biology. The resource focused webinars are more computationally advanced and you will need prior knowledge of programmatic access and common programming languages. If you are new to programmatic access we recommend that you watch the introductory webinar first.
What will I achieve?
By the end of the course you will be able to:
- List available EMBL-EBI webservices
- Describe processes that can be performed using EMBL-EBI RESTful APIs
- Know where to find help, documentation and get support
- Access example scripts
What resources do I need?
There are no specific resources required to watch the webinars, however some webinars have example scripts which may require further software installation.
DOI: 10.6019/TOL.EBIprogrammatically-w.2017.00001.1
Course contents
- Introduction to EMBL-EBI resources
- Introduction to programmatic access
- EBI Search, programmatically
- Europe PMC, programmatically
- Ensembl, programmatically
- UniProt, programmatically
- InterPro, programmatically
- PDBe, programmatically
- ChEMBL and UniChem, programmatically
- Sequence analysis tools, programmatically
- EVA, programmatically
- MGnify, programmatically
- Open Targets, programmatically
- Summary
- Your feedback
How and when to access the course
All our courses are designed with flexibility in mind. You can access them for free at any time, just click on the "Enter Course" button.
It is up to you how you use the course; you can either study the full course or you can focus on sections that are relevant to you. To jump between sections, use the navigation bar on the left or the arrows at the bottom of the page. You can also choose whether to complete the course in one go, or over several visits.
The average time to read through the main body of the course is 3 hours (not including exercises and external links). The time may vary depending on your prior knowledge and how you choose to work through the course.
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You can track your progress and keep a record of any completed learning by creating an account. This will give you a 'My learning' page, which will have three main tabs to help keep track of your progress:
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In progress: The courses which you have started reading will be added to your 'In progress' tab. Use the 'Mark as complete' button at the end of the course pages to get started.Your ‘In progress’ tab gets updated as you progress through the course and will show you what percentage of the course you have finished and will let you resume the course from where you left on your last visit.
Completed: The courses which you have finished entirely will be added to the 'Completed' tab.
The results you gain from completing quizzes and other interactive content will also be added to your My learning page.
You can register anytime here or click a 'Favourite' or 'Mark as complete' button to start tracking your progress.
You can still access all the online tutorials and interactive content if you do not register, but you will not be able to track your progress.
Making the most of the course
Learning something new takes time and practice. We encourage you to:
- Use the activities and quizzes to help you check your learning, recall and apply key concepts. Look out for these icons
Activities | Quizzes | Videos |
- Revisit sections as and when you need them. Bookmark relevant pages in your browser or use the navigation panel to jump the relevant section.
Getting help and providing feedback
If something isn’t working or if you have a question get in touch by contacting us at trainonline@ebi.ac.uk
Tell us what you thought about the course (both good and bad!) using the “Feedback and help” button found at the top of each page.
Your feedback helps us ensure we are providing training that is relevant and useful for you.
For help and support on EMBL-EBI resources you can contact the helpdesk directly.
Learn more
You can explore other training on offer from EMBL-EBI on our website. We offer online courses, webinars, face-to-face courses and offsite training.