Samuel Lampa presented at Go Stockholm Conference

6 Oct, 2018. Samuel Lampa presented on the Go Stockholm 2018 conference, on the topic of “Using Flow-based programming to write tools and workflows for Scientific Computing in Go” (Slides available in the link). The talk described first som ...

Samuel Lampa successfully defended his PhD thesis: Reproducible Data Analysis in Drug Discovery with Scientific Workflows and the Semantic Web

28 Sep, 2018. Today, Samuel Lampa from the group successfully defended his thesis, titled: “Reproducible Data Analysis in Drug Discovery with Scientific Workflows and the Semantic Web“ CONGRATULATIONS SAMUEL! Supervisor: Assoc Prof. Ola Spj ...

CANCELLED: Dr. Konrad Hinsen presenting on "Building trust in Computational Science: From Reproducible to Verifiable Computer-aided Research"

29 Aug, 2018. Updated Sep 25: This event is cancelled due to scheduling obstacles! Time and Location Date: September 27, 2018, 15.00-16.00 (Attn: Time updated!) Location: Triple room (click for map), SciLifeLab, Biomedical Center (BMC), Husargatan 3, U ...

Upcoming Dissertation: Reproducible Data Analysis in Drug Discovery with Scientific Workflows and the Semantic Web

29 Aug, 2018. On September 28, Samuel Lampa from the group will defend his thesis, titled: “Reproducible Data Analysis in Drug Discovery with Scientific Workflows and the Semantic Web“ Supervisor: Assoc Prof. Ola Spjuth, Uppsala University ...

Summer-BBQ of 2018

14 Jun, 2018. This year again there was a summer-BBQ at Ola’s place. On June 14th the weather was very nice, and no one left hungry! This will definitely be a recurring event! ...

Niharika Gauraha presenting on COPA2018

12 Jun, 2018. Niharika Gauraha in the pharmb.io group presented her work at the conference Conformal Prediction and Probabilistic Predictions with Applicationsi (COPA) 2018 Conference website: http://www.clrc.rhul.ac.uk/copa2018/ Conformal Prediction in ...

Prof. Roland Grafström presenting on 'modeling adverse outcome by omics-driven informatics'

27 May, 2018. Professor Roland Grafström (Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden and Misvik Biology, Turku, Finland) will visit us at BMC and give a presentation. Entering the era of “Big Data”: defining and modeli ...

Pharmb.io co-organizing Linked Data Symposium

15 Feb, 2018. pharmb.io is this year co-organizing a symposium named “Linked Data in Sweden”. It is a symposium held annually with the aim to bring people together to share experiences around Linked Data. This year, the event is hosted by the ...

Open PhD student position in Applied Mathematics: Machine Learning and Conformal Prediction, applied to Drug Discovery and Cancer Diagnostics

6 Jan, 2018. There is now an opportunity to apply for a PhD position in Applied Mathematics with a project from our group with the title: “Machine Learning and Conformal Prediction, applied to Drug Discovery and Cancer Diagnostics”. The PhD ...

Alexander Kensert introducing his Masters project

4 Dec, 2017. Alexander Kensert gave an introductory presentation on his Masters thesis project in our group, with the title: “Building Supervised In Silico Models Using Hashed and Unhashed Morgan Fingerprints”. ...

Phil Harrison new PhD Student in our group

22 Nov, 2017. We welcome Phil Harrison as new PhD Student in our group. Phil obtained his first PhD in marine biology in 2006 studying the population dynamics of grey seals. Between 2006-2016 he undertook several research projects modelling wildlife popu ...

New GopherData post on Go-based workflow tools

10 Nov, 2017. Samuel and Jon from the group contributed to a post on the GopherData website together with Daniel Whitenack from the Pachyderm team, providing a brief overview of the growing ecosystem of workflow tools in bio- and cheminformatics implemen ...

Ola Spjuth presenting PhenoMeNal at Nordic Tryggve2 Kickoff

7 Nov, 2017. Ola Spjuth presented at the Nordic Tryggve2 Kickoff, 7 November 2017 in Märsta, Sweden. Tryggve 2 is a project within The Nordic e-Infrastructure Collaboration (NeIC), consisting of the Nordic countries Sweden, Finland, Norway and Denmark a ...

Pharmb.io group joining Glenna2 project with experiences and use cases from PhenoMeNal

6 Nov, 2017. Our research group will contribute to the Glenna2 project, an activity within the Nordic e-Infrastructure Collaboration (NeIC). We will contribute with experiences and use cases from the PhenoMeNal-H2020 project, and the focus is on making ...

HASTE project workshop at AstraZeneca, Mölndal

24 Oct, 2017. The HASTE project partners visited the AstraZeneca site in Mölndal for a 2-days workshop. There were discussions on project progress, recruitment, plans ahead, and a visit to see the many different (high content) microscopes at AstraZeneca. ...

Ola Spjuth presenting on de.NBI Symposium 2017 at Bielefeld University

23 Oct, 2017. Ola Spjuth presented at the de.NBI Symposium 2017 “The Future Development of Bioinformatics in Germany and Europe”. The symposium was held at the Center for Interdisciplinary Research (ZiF) of Bielefeld University from October 23-25, 2017. ...

Presentation at DevFest Siberia 2017

4 Oct, 2017. Jon Ander Novella presented at DevFest Siberia 2017, on the topic of “Scalable and reproducible bioinformatics workflows with Pachyderm”. Further details about the talk can be found at our previous blog post or at the conferenc ...

Presentation at the 2017 Imperial College Computing Student Workshop

3 Oct, 2017. Marco Capuccini presented KubeNow at the 2017 Imperial College Computing Student Workshop (ICCWS2017). KubeNow is a cloud agnostic platform for microservices, based on Docker and Kubernetes. Slides are availabe here. ...

OpenRiskNet Workshop in Uppsala 25-26 Sept 2017

26 Sep, 2017. On 25-26 Sept 2017 our group organized a workshop on microservices development with a large focus on Kubernetes/OpenShift and how we can establish a CICD system within the OpenRiskNet project. The meeting was attended by 16 people from 8 Eu ...

Presentations and Tutorials at 'Big Data Training School for Life Sciences'

21 Sep, 2017. The pharmb.io and caramba.clinic teams were heavily involved in the COST-CHARME ‘Big Data Training School for Life Sciences’, 18-22 September 2017 in Uppsala, Sweden. Ola Spjuth was member of the Scientific Committee and also ha ...

Jon Ander Novella to speak at DevFest Siberia 2017

24 Aug, 2017. Jon Ander Novella will present at DevFest Siberia 2017, on the topic of “Scalable and reproducible bioinformatics workflows with Pachyderm”. Abstract Computational biology is complex not only because of the increasing amounts o ...

The pharmb.io summer-BBQ of 2017

5 Jul, 2017. The yearly summer-BBQ took place July 5th at Ola’s place. All sorts of food was grilled, and many people brought something extra for the table. In short, a really nice evening! ...

Special Issue in J Cheminformatics on "Novel applications of machine learning in cheminformatics"

5 Jul, 2017. Ola Spjuth is guest editor for a new special issue in J. Cheminformatics with the topic “Novel applications of machine learning in cheminformatics”. Looking forward to exciting submissions! ...

Open position: PhD student in bioinformatics with focus on machine learning on large-scale image data

22 Jun, 2017. Our group is participating in the HASTE project (Hierarchical Analysis of Temporal and Spatial Image Data) which is recruiting two PhD students. One of the positions will be placed in our lab with focus on machine-learning with quantifiable ...

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Pharmb.io running team 'Metab elite' completes Blodomloppet race

19 Jun, 2017. On 2017-05-18, the pharmb.io running team ‘Metab elite’ were able to complete the Blodomloppet race over 10 km! When enjoying the well-deserved picnic after the finish line, the team was looking ahead to future races… Re ...

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COPA2017: Conformal Prediction and Probabilistic Predictions with Applications conference in Stockholm

13 Jun, 2017. The 6th Symposium on Conformal Prediction and Probabilistic Predictions with Applications conference (COPA2017) was held at Karolinska Institutet, Stockholm, on June 13-16 2017. Ola Spjuth was local organizer and also chaired the session &l ...

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Open position: Postdoc/Researcher in Bioinformatics with focus on Machine Learning and Image Analysis

8 May, 2017. Our group is participating in the HASTE project (Hierarchical Analysis of Temporal and Spatial Image Data) which is recruiting up to three postdocs or researchers in Computerized Image Analysis, Scientific Computing and Bioinformatics. One ...

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Paper published: E-Science technologies in a workflow for personalized medicine using cancer screening as a case study

24 Apr, 2017. After 3 years, our paper on e-Science in cancer screening is finally published by J Am Med Inform Assoc (JAMIA). Abstract Objective: We provide an e-Science perspective on the workflow from risk factor discovery and classification of disea ...

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New supercomputers at Uppsala University and SciLifeLab enables data-intensive bioinformatics on sensitive data

20 Apr, 2017. Today the two supercomputers Bianca and Rackham are inaugurated at Uppsala University. Read the news article at SciLifeLab, interviewing Ola Spjuth in his role as Head of Compute and Storage facility at SciLifeLab. See also the Inauguration ...

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Marco Capuccini and Stephanie Herman presenting on PhenoMeNal Workflow Workshop, 4-5 April, in Halle, Germany

4 Apr, 2017. Marco Capuccini and Stephanie Herman presented at the “PhenoMeNal Workflow Workshop”, 4-5 April, in Halle, Germany. The presentation covered a lot of the work that has been going on in the Uppsala team on workflows in “Phe ...

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Ola Spjuth presented at CloudBeer 2017: 'The case for cloud computing in Life Sciences'

30 Mar, 2017. Ola Spjuth held a presentation “The case for cloud computing in Life Sciences” at CloudBeer 2017 on March 23rd: The case for cloud computing in the life sciences There is a recording from the event available (also embedded belo ...

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Our paper: Large-scale virtual screening on public cloud resources with Apache Spark, got published in the Journal of Cheminformatics

7 Mar, 2017. Abstract Background Structure-based virtual screening is an in-silico method to screen a target receptor against a virtual molecular library. Applying docking-based screening to large molecular libraries can be computationally expensive, h ...

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Video from Marco Capuccinis talk at Spark Summit now online

14 Feb, 2017. As we have posted before, our colleague Marco Capuccini has been presenting at Spark Summit East 2017, with the title “EasyMapReduce: Leverage the power Of Spark And Docker To scale scientific tools In MapReduce fashion“ (click ...

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Our project: 'Hierarchical Analysis of Temporal and Spatial Image Data' will receive funding by SSF

9 Feb, 2017. Ola Spjuth is co-PI in the project ‘Hierarchical Analysis of Temporal and Spatial Image Data’ that received 29 MSEK from SSF for the period 2017-2021. Press release from Uppsala University Press release from SSF Abstract from th ...

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Presentation 'Analyzing Big Data in Medicine with Virtual Research Environments and Microservices' by Ola Spjuth on Uppsala University official YouTube Channel

26 Jan, 2017. This presentation was given by Ola Spjuth in the ‘Current Challenges in Biomedical Information Technology - Big Data in Medicine’ symposium series at the IT-department at Uppsala University. The slides are available from “ ...

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Marco Capuccini to present at Spark Summit East 2017

20 Dec, 2016. Marco Capuccini will present at Spark Summit East 2017: “EasyMapReduce: Leverage the power Of Spark And Docker To scale scientific tools In MapReduce fashion” Abstract: High-throughput methods in various scientific fields produc ...

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