Event by Novo Nordisk Foundation Science Cluster

    Workshop - Microbiome data interpretation

    Studying microbiomes using metagenomic sequence data is a topic of major scientific importance, for example due to the impact of human microbiota in human health, or the impact of environmental microbiota in our daily life. Scientists are now generating an exponentially increasing amount of microbiome-derived sequence data, and this trend is expected to continue as sequencing costs are currently falling. The major bottleneck in microbiome studies is to interpret this complex data in the context of existing literature and datasets, which can sometimes take years. Thus there is an urgent need to accelerate the interpretation phase of microbiome data analysis. Text mining can help with this by systematically annotating the biomedical literature with organisms, processes, environments and associations among them. Interactive text-mining tools can furthermore be used to speed up standards-compliant annotation of environmental descriptors for existing datasets, which is important to facilitate comparisons. However, most microbiome analysts are unaware of the power of text mining. The proposed practical course will provide hands-on training to participants in handling metagenomic sequence data, generating taxonomic/functional summaries, performing statistical analysis based on a case-control scenario as example, and interpreting the results using automated text mining tools. Participants will gather new knowledge about microbiome analysis and text mining. They will learn how to use state-of-the-art analysis tools to efficiently interpret results. Participants will also learn how to use computerome, the largest supercomputer in Denmark, to analyse large microbiome datasets. The aim is that this will speed up data interpretation and knowledge generation to match the fast pace with which raw data are generated.

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    25-26 October 2017


    Manimozhiyan Arumugam
    Lars Juhl Jensen
    Luis Pedro Coelho
    Evangelos Pafilis

    Course requirements

    The participants should be actively working with microbiome data and are expected to have some prior experience with computational data analysis but not specifically with text mining. All participants need to register with a motivation letter stating their experience.

    It is mandatory to bring your own computer.

    Read more about the speakers

    Luis Pedro Coelho, PhD, Post-doctoral researcher, EMBL-Heidelberg, Germany. coelho@embl.de

    Dr. Coelho is the main developer of the “ngless” microbiome analysis pipeline, which will be used on the course.

    Evangelos Pafilis, PhD, Research scientist, Hellenic Center for Marine Research, Crete, Greece. pafilis@hcmr.gr

    Dr. Pafilis played a key role in developing all of the text-mining tools that will be used on the second day of the course, namely the SPECIES/ORGANISMS and ENVIRONMENTS named entity recognition systems, the EXTRACT interactive annotation tool, and the seqenv tool for automatic annotation of microbial samples.


    Registration and submission of a motivation letter is open to all levels of participants: MSc students, PhD students, postdocs and PIs. Registration is completely free of charge, but mandatory. Participants will be selected in order to ensure a balanced and diverse participant field.

    Registration is open until 1 August, 2017. The scientific committee will send out a confimation to the selected participants on August 15th, 2017.

    Scientific committee

    Manimozhiyan Arumugam

    Group Leader, Associate professor

    NNF Center for Basic Metabolic Research, Section for Metabolic Genetics

    Lars Juhl Jensen

    Group Leader, Professor

    NNF Center for Protein Research, Disease Systems Biology Program


    Day 1
    8:30 am Welcome and introduction to the course
    9:00 am Lecture 1: Introduction to microbiome analysis
    10:30 am Coffee break
    11:00 am Lecture 2: Introduction to text mining
    12:30 pm Lunch
    1:30 pm Tutorial 1: Hands-on introduction to text-mining tools
    3:00 pm Coffee break
    3:30 pm Tutorial 2: Hands-on introduction to metagenomic tools
    5:30 pm Networking dinner
    Day 2
    8:30 am Workshop 1: Microbiome data analysis using case/control design
    10:30 am Coffee break
    11:00 am Workshop 1: Microbiome data analysis using case/control design (continued)
    12:30 pm Lunch
    1:30 pm Workshop 2: Interpretation of microbiome results using text mining tools
    3:00 pm Coffee break
    3:30 pm Workshop 2: Interpretation of microbiome results using text mining tools (continued)
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    What are my transport/parking options getting to the event?

    1. There is no car parking available for participants at the location. It is up to the participant to find a valid public parking space.

    2. Cyclists can use one of the many bicycle stands on campus or the basement bicycle parking below the Maersk Tower.

    How do I get to the meeting room?

    Address: Blegdamsvej 3B, 2100 Copenhagen.

    Room: Maersk Tower, 15th floor, Meeting room 7.15.149.

    Transportation: Bus no. 3A stops on Blegdamsvej (stops: Skt. Hans Torv or Rigshospitalet Syd) and bus no. 6A stops on Tagensvej (stop: Rigshospitalet Syd).


    1. Enter the Maersk Tower from Blegdamsvej through revolving door
    2. On your left, find elevators ca. 15 meters away from the revolving door (Elevators A to E)
    3. Find the numberpad with buttons on the wall next to the elevators (You have to enter your destination floor here, and not inside the elevator)
    4. Enter 15 and find out which elevator the system directs you to
    5. Walk to the specified elevator, wait for it, and enter (you cannot use the buttons inside to specify the floor)
    6. Exit at 15th floor, turn right and follow directions for Room 7.15.149.

    Where can I contact the organizer with any questions?

    Contact Sophie Labrosse at sfeb@novo.dk

    How do I cancel my participation?

    Please help us respecting our speakers, as well keeping track of the numbers and optimize lecture and catering to the audience by cancelling as soon as you know that you exceptionally will not be able to make it. Send an email to Sophie Labrosse (sfeb@novo.dk).