Now accepting applications for our new Postdoctoral Fellowship in Computational Medicine program

Application Deadline: Sept. 1, 2019. Apply here.


Steven Niederer, King’s College London, “Applying Cardiac Modelling to Study Drugs, Devices and Diagnosis”
Apr 30 @ 11:00 am – 12:00 pm

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“Applying Cardiac Modelling to Study Drugs, Devices and Diagnosis”

Dr. Steven Niederer received his DPhil in computer science from the University of Oxford in 2009, where he developed a detailed biophysical model of the rat heart. At the end of his DPhil he was awarded a research fellowship from the UK Engineering and Physical Sciences Research Council (EPSRC) to create pre-clinical models of heart failure. In 2010, he was appointed as a lecturer at King’s College London (KCL). At KCL he set up a research group focused on the clinical translation of cardiac models. Since joining KCL he has received a UK research council fellowship to work on the clinical translation of cardiac models to study heart failure, funding from the British Heart Foundation to work on simulating heart failure, ventricular arrhythmias and atrial fibrillation and industry support from pharmaceutical (Pfizer), device (EBR systems, Abbot, Boston Scientific, Medtronic) and imaging (Siemens) companies to use computer models for commercial applications. The combination of engineering, clinical and industrial research drives the translational focus of the group.


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“Applying Cardiac Modelling to Study Drugs, Devices and Diagnosis”

The ability to measure the heart, its shape, its structure and its function across multiple spatial and temporal scales continues to grow. Interpreting this data remains challenging. Computational biophysical models of the heart allow us to quantitatively link and interpret these large disparate data sets within the context of known cardiac physiology and invariable physical constraints. Within these models, we can infer unobservable states, propose and test new hypothesis and predict how systems will respond to challenges increasing our ability to interrogate and understand biological systems. We are increasingly applying this approach to modelling human hearts to investigate clinical applications. In this presentation, I will give an overview on our modelling work simulating anthracycline-induced heart failure, how we are using models of individual patients to study cardiac resynchronisation therapy and how we are using simulations to characterise the anatomy and pathophysiology of atrial fibrillation patients. Finally, I will present some of our preliminary results on simulating the four-chamber heart to begin simulating the interactions between atrial and ventricular function.


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Foundations of Computational Biology and Bioinformatics II Poster Session 2019
May 1 @ 6:00 pm – 8:00 pm

This event sponsored by the Institute for Computational Medicine and the Department of Biomedical Engineering, features student projects for Foundations of Computational Biology and Bioinformatics II, a biomedical engineering course taught by Professor Rachel Karchin, PhD, William R. Brody Faculty Scholar, and ICM Core Faculty Member. For a complete list of student projects, view the event flyer .

Computational Medicine in the Cloud
Jun 10 @ 9:00 am – Jun 11 @ 6:00 pm

We are pleased to announce the first ever Computational Medicine in the Cloud Hackathon! NCBI will help run a bioinformatics hackathon in Baltimore, Maryland hosted by the Johns Hopkins University.

We’re specifically looking for folks who have experience in working with complex haplotypes, complex disease, precision medicine, and similar genomic analysis. If this describes you, please apply! This event is for researchers, including students and postdocs, who are already engaged in the use of bioinformatics data or in the development of pipelines for large scale genomic analyses from high-throughput experiments (please note that the event itself will focus on open access public human data).

Potential topics include:

  • Coherent-phenotype mapping to haplotypes
  • Mapping haplotype blocks to ontologies
  • Structural Variants in Health and Disease
  • Haplotypes and RNA-seq
  • Complex Variant Structure
  • Annotation Structures for Complex Variants
  • Visualization of Complex Variants

Hackathon Logistics

The hackathon runs from 9 am – 6 pm each day, with the potential to extend into the evening hours each day. There will also be optional social events at the end of each day. Working groups of five to six individuals, with various backgrounds and expertise, will be formed into five to eight teams with an experienced leader. These teams will build pipelines and tools to analyze large datasets within a cloud infrastructure. On both days, we will come together to discuss progress on each of the topics, bioinformatics best practices, coding styles, etc.

There will be no registration fee associated with attending this event.

Note: Participants will need to bring their own laptop to this program. No financial support for travel, lodging, or meals is available for this event.



Datasets will come from open access public repositories, with a focus on a number of trios produced by long read sequencing as a base graph and short read datasets in the sequence read archive that have been ported to cloud infrastructure, as well as derivative contigs of the above.



All pipelines and other scripts, software, and programs generated in this hackathon will be added to a public GitHub repository designed for that purpose.

Manuscripts describing the design and usage of the software tools constructed by each team may be submitted to an appropriate journal such as the F1000Research hackathons channel, BMC Bioinformatics, GigaScience, Genome Research or PLoS Computational Biology. Ideally, we will present a graph genome, a number of protocols for associating short read omics data with it, and some derived datasets (e.g. variant calls) from such protocols.



To apply, please complete this form. Initial applications are due on May 22, 2019 by 3 pm EDT. We will select participants based on the experience and motivation they indicate on the form.

Prior participants and applicants are especially encouraged to apply. The first round of accepted applicants will be notified on May 24 by 3 pm EDT, and will have until noon EDT on May 28 to confirm their participation (especially qualified applicants or those traveling internationally may receive acceptances earlier). If you confirm, you must be willing to commit to both days of the event, as confirming and not attending prevents other data scientists from attending this event.



Entrants retain ownership of all intellectual property rights (including moral rights) in the code submitted to as well as developed in the hackathon. Employees of the U.S. Government attending as part of their official duties retain no copyright in their work and their work is in the public domain in the U.S.

The Government disclaims any rights in the code submitted or developed in the hackathon.

Participants agree to publish the code and any related data in GitHub.

For more information, or with any questions, please contact Ben Busby (

Novartis Quantitative Sciences Academia-to-Industry Hackathon
Aug 12 @ 9:00 am – Aug 23 @ 5:00 pm

JHU - Institute for Computational Medicine