HASTE: Hierarchical Analysis of Spatial and Temporal Data

The HASTE project, a SSF-funded project on computational science and big data, takes a holistic approach to new, intelligent ways of processing and managing very large amounts of microscopy images to leverage the imminent explosion of image data from modern experimental setups in the biosciences. One central idea is to represent datasets as intelligently formed and maintained information hierarchies, and to prioritize data acquisition and analysis to certain regions/sections of data based on automatically obtained metrics for usefulness and interestingness.

The project is a collaboration between the Wählby lab (PI),  Hellander lab (co-PI), both at the Department of Information Technology, Uppsala University, the Spjuth lab (co-PI) at the Department of Pharmaceutical Biosciences, Uppsala University,  the Nilsson lab at the Department of Biochemistry and Biophysics at Stockholm University and SciLifeLab, Vironova AB and AstraZeneca AB.

Read more on the project webpage.


Postdoc in Scientific Computing/Applied Cloud Computing

We are looking for a talented individual to join our efforts on creating smart and scalable cloud services to support simulation-driven scientific discovery via large-scale computational experiments such as parameter sweeps. This is a classic and very important problem that we will approach in new ways, leveraging recent advances in cloud computing, data-intensive computing and machine learning. See the full advertisement here (Deadline Sept. 1):


The successful candidate will contribute to the interdisciplinary research group Distributed Computing Applications (DCA) at the Department of Information Technology, Uppsala University.



Fredrik Wrede joins the group

We are very happy to welcome Fredrik Wrede, MSc. in Bioinformatics, to the group. Fredrik was accepted as a PhD student in CIM, the Center for Interdisciplinary Mathematics. His project will center around intelligent cloud services for processing and making sense of massive amounts of data, for example generated by large computational experiments in systems biology such as parameter sweeps.  The project is an interdisciplinary collaboration with the Spjuth lab on data-intensive and translational bioinformatics.


Göran Gustafsson prize

Last week brought some great news. I am awarded the Göran Gustafsson Prize 2016 from the Gustafsson Foundation (KTH/UU). In the proposed project titled Smart Services for Scientific Discovery we will look into new and more productive ways to combine simulation software and cloud computing infrastructure to build intelligent applications for e.g. exploring an underlying model’s essential behavior.

Open Posititions: up to two PhD students

(Call for applications is closed. )

We are expanding the group with up to two PhD students in the areas of Applied Mathematics and Applied Cloud Computing:

Interested candidates are welcome to contact me for more information.