Biomed-IT Research Arena
May 15: Lunch seminar 12.00 in 2446 with Adam Ameur and Niclas Jareborg who talk about the data processing challenges associated to the SweGen project that aims to map genetic variation in Sweden. Register here
We have been undertaking one of the largest human whole-genome sequencing project in Sweden to date; the generation of a reference database that reflects the genetic structure of the population. 1000 individuals were selected for this “SweGen” project, sampled to cover the genetic variation within Sweden. This database is the first of its kind in Sweden and is needed both for disease association studies and for evaluating the relevance of genetic alterations detected during clinical diagnostic analyses.
Over 200 TB of raw sequence data have been generated within the SweGen project and the analysis of all this data has posed a great challenge. Moreover, since the genetic data contains sensitive personal information, special measures have been taken to make sure the data is handled according to personal integrity regulations. We have established a resource (swefreq.nbis.se) for sharing aggregated genetic information in the dataset that is of great value for other researchers, without revealing the underlying personal information. We are also establishing ways of sharing the individual data with other researchers that have legitimate reason to access it.
May 31: AIMday The BiomedIT Research Arena will organise an AIMday focusing on the use of machine learning in life science and medicine at Navet, BMC, Uppsala University. See the aimday homepage.
June 8: Seminar by Anne Carpenter (Broad Institute of Harvard and MIT, US) 13:15 at SciLifeLab, triple room in Navet, BMC, E10:1309
A picture is worth a million data points: Tackling world health problems via cell morphology
Health Care Science 2018
Forte and the Swedish Research Council announce programme grants for health care research, amounting to SEK 180 million. In this joint call for proposals, the grants will amount to SEK 3-5 million per year for up to six years.
News from outside the department
Post Doc position, computer models of mechanical structures in interventional radiology at CRI Nancy, France
Innovative Medicines Initiative (an initiative from the European Union) will have an upcoming call titled Development of a platform for federated and privacy-preserving machine learning in support of drug discovery.
Projects within Biomedical Information Technology
We run a wide variety of projects within the area of Biomedical Information Technology. Here we list brief summaries of ongoing projects.
Use the checkboxes to select which types of projects to display.
April 26 2018: Workshop for the initiation of new collaborations with GE Healthcare. Participating speakers from GE as well as the IT department, hosted by the BiomedIT arena. 9.00-12.00
Inauguration of Uppsala MedTech Science & Innovation. Video of the event.
Workshop on current Biomed-IT projects in Uppsala
- HASTE: Hierarchical Analysis of Spatial and Temporal Data From intelligent data acquisition via smart data-management to confident prediction Abstract
- Carolina Wählby, Division of Visual Information and Interaction, Dept. of IT, UU
- Andreas Hellander, Division of Scientific Computing, Dept. of IT, UU
- GE Software for Biopharmaceuticals Abstract
- Key Hyckenberg, Staff Software Engineer, Life Sciences, GE Healthcare
- Haptics-Assisted Cranio-Maxillofacial Surgery Planning using Interactive 3D Image Segmentation and Visualisation Abstract
- Ingela Nyström, Division of Visual Information and Interaction, Dept. of IT, UU
- Andreas Thor, Oral & Maxillofacial Surgery, Dept. of Surgical Sciences, UU
- Next Generation Sequencing of Ancient DNA - Challenges and Opportunities Abstract
- Torsten Günther, Dept. of Organismal Biology, UU
- Health and Biodiversity in the Era of Data-Driven Research Abstract
- Björn Nystedt, National Bioinformatics Infrastructure Sweden, NBIS
Site visit to the Radiology department
There will be a guided tour where we get information about, and visit, different acquisition systems such as X-ray, CT, PET, Angio and MR. During the site visit, we will also get a presentation, and demo, of the information systems PACS and RIS.
Host: Per Albrektsson
Venue: We meet by entrance 85
Date and time: May 5, 13:00-16:00
Maximum number of participants: 25
Lunch seminars on current challenges in biomedical information technology Spring 2017
March 29, 12:00-13:00, Room ITC2446.
Computational challenges in the era of modern genomics: the problems
Manfred Grabherr, PI at IMBIM, UU
Computational challenges in the era of modern genomics: the solutions
Neda Zamani, researcher in the Grabherr group
Register no later than March 27 for a free sandwich
Lunch seminars on current challenges in biomedical information technology Autumn 2016
NEW: Videos from the lectures are now available on Uppsala University's YouTube channel. See links in the information below.
Digital Health. October 6, 12:00-13:00, Room ITC2446.
- Dag Nyholm, Medical Doctor, Neurology, Department of Neuroscience, UU. Video.
- Maria Hägglund, Senior Researcher, Health Informatics Centre, KI. Video.
Personalized Care Outside the Hospital. October 20, 12:00-13:00, ITC2344.
- Per-Olof Sjöberg, head of the Business and Innovation area eHealth, SICS. Video.
- Helena Grönqvist, Researcher and Research Coordinator, U-CARE, Dept. of Public Health and Caring Sciences, UU. Video.
Big Data in Medicine. November 17, 12:00-13:00, Room ITC2446.
- Ola Spjuth, Associate Professor, Dept. of Pharmaceutical Biosciences, UU. Video.
- Emma Lundberg, Associate Professor, Human Protein Atlas, KTH. Video.
Slides from the Biomed-IT workshop May 18, 2016
Workshop on Biomedical Information Technology, including final presentations of SPARC Projects.
- Design for Improved Patient Safety: Resilience Engineering and Sociotechnical Systems Design in Intensive Care. Speaker: Anders Jansson
- Automated multiscale analysis of TEM images for improved cost-effective diagnosis of cilia disorders. Speaker: Ida-Maria Sintorn
- Inference and Data-driven Modeling of population of Cells. Speaker: Stefan Engblom
- Director of Research and Education, Professor Uppsala University Hospital. Speaker: Sune Larsson
- Vice-rector of the Disciplinary Domain of Science and Technology. Speaker: Johan Tysk
- Mathematical Modeling of Neural and Behavioral Response in Deep Brain Stimulation. Speaker: Alexander Medvedev
- Computerized Image Analysis for Ophthalmologic Applications. Speaker: Filip Malmberg
- Chopsticks: Motion Sensors for Medical Diagnosis and Habilitation. Speaker: Edith Ngai