Presenting at ELRIG conference: Advances in Cell-Based Screening in Drug Discovery 2022
12 May, 2022. On 10-12 May Ola, Amelie, Christa, Jonne and Martin from the pharmb.io team visited the ELRIG conference Advances in Cell-Based Screening in Drug Discovery 2022. Ola had an oral presentation on the third day whereas Jonne, Christa and Ameli ...
20 Dec, 2021. Funded by an infrastructure grant from the Swedish Research Council, our research group at Uppsala University is now establishing a new node as part of the Chemical Biology Consortium Sweden, a national infrastructure for chemical biology. ...
Just published: 'A phenomics approach for antiviral drug discovery' in BMC Biology
3 Jul, 2021. Our latest work “A phenomics approach for antiviral drug discovery” has now been published at BMC Biology! Jonne Rietdijk, Marianna Tampere, Aleksandra Pettke, Polina Georgiev, Maris Lapins, Ulrika Warpman-Berglund, Ola Spjuth, Marjo-Riitt ...
Amelie Wenz joins the research group as new PhD Student
3 Jul, 2021. We welcome Amelie Wenz who recently started as a PhD Student in our group! What is your education, and what have you done earlier in your career? I started my education by studying Biological Science at the University of Konstanz in German ...
24 Jun, 2021. We are excited to announce that Christa Ringers has received a prestigious 3-year mobility grant from Norwegian Research Council to join our team at Uppsala University as a PostDoc for 2 years and then continue the project at Norwegian Univ ...
David Holmberg joins the research group as new PhD Student
3 May, 2021. We welcome David Holmberg who recently started as a PhD Student in our group! David will work in the Autonomous Phenomics project. What is your education, and what have you done earlier in your career? Alright, so I am a graduate from Lund ...
22 Feb, 2021. There is now an opportunity to apply for a PhD position in Applied Mathematics with a project from our group with the title: “Autonomous Decision Making in Automated Cell Profiling for Drug Discovery Applications”. The PhD stud ...
Open positions for 2 PhD students and 1 PostDoc in our lab
1 Jan, 2021. After being awarded 2 grants from the Swedish Research Council, we are now strengthening our team to work towards autonomous phenomics and precision cancer medicine.For more information about the project and research group, see https://pha ...
Our HASTE team wins the Adipocyte Cell Imaging Challenge organized by AI Sweden and AstraZeneca
23 Nov, 2020. We are very happy to announce that the HASTE team has emerged as the winners to the Adipocyte Cell Imaging Challenge that was organized by AstraZeneca and AI Sweden as a challenge to the AI community to solve the problem of labeling cell i ...
Open position as Data Engineer in our lab
10 Nov, 2020. We are looking for a skilled Data Engineer to join our team! Tasks In collaboration with other researchers, develop, implement and test systems for AI-controlled automated microscopes. The task includes interacting directly with the micros ...
Swedish Research Council will fund our project 'Autonomous Phenotypic Drug Profiling'
29 Oct, 2020. We are very happy to announce that the Swedish Research Council has decided to fund the project Autonomous Phenotypic Drug Profiling under the call Project Grant 2020 for Natural end engineering science (VR-NT 2020) where Prof. Ola Spjuth ...
Ola Spjuth interviewed at the faculty
20 Oct, 2020. Group leader Ola Spjuth was interviewed and presented at the faculty in a post entitled Self-learning machines take the step into drug discovery Link to the full article here. ...
1 Oct, 2020. For a PhD or Postdoc involved in a research project at the Centre for Digital Life Norway or is a member of its research school, there is now an opportunity to apply for a three-year researcher project with international mobility to join o ...
Jordi Carreras-Puigvert joins the research group
24 Sep, 2020. We welcome Jordi Carreras-Puigvert who recently started as a Lecturer in our group. Jordi is a strategic recruitment from Karolinska Institutet, and he will establish his own research topic in the group working on cancer drug screening. Ex ...
Andreina presenting at 19th workshop on Constraint Modelling and Reformulation
9 Sep, 2020. Andreina Francisco in our team presented on 2020-09-07 a talk with the title A Constraint Programming Approach to Microplate Layout Design at the The 19th workshop on Constraint Modelling and Reformulation in Louvain-la-Neuve, Belgium. A vi ...
Ola Spjuth appointed Professor in Pharmaceutical Bioinformatics
22 Aug, 2020. Group leader Ola Spjuth was appointed Professor in Pharmaceutical Bioinformatics at Department of Pharmaceutical Biosciences, Uppsala University, from July 1st, 2020. ...
Andreina Francisco new Postdoc in the group
20 Jul, 2020. We welcome Andreina who recently started a 2-year postdoc position in our group in the project AI methods for decision making in automated biological laboratories. The position is part of the strategic research area effort eSSENCE´s PostDo ...
New project for profiling coronavirus-infected cells funded by SciLifeLab and KAW!
6 May, 2020. Our recent grant application Multi-level profiling of Coronavirus-infected cells by combining Viral Entry Assays, Cell Painting, and DrugSEQ was awarded 500 KSEK by SciLifeLab and Knut och Alice Wallenbergs Stiftelse in a joint effort with ...
Postdoc position available: AI methods for large-scale microscopy imaging
20 Mar, 2020. We are currently looking for an ambitious, highly motivated Postdoc with a good background in AI and imaging to join our research group where we have built up a robotized cell profiling system with high-content microscopy imaging as primar ...
NeIC Glenna project visits our group
10 Mar, 2020. The NeIC project Glenna (https://neic.no/glenna/) had its final meeting in Uppsala on March 10, 2020. Our group’s involvement has been in the project towards establishing a Nordic AI collaboration, and in particular on: 1) Evaluating ...
2 Mar, 2020. 5 people of our group visited the conference: Phenotypic Screening, High-Content Analysis and AI: Overcoming the Challenges that was held March 2-3rd at AstraZeneca, Gothenburg, Sweden. Ola Spjuth shared the session AI and Machine Learning ...
Postdoc position available: AI methods for decision making in automated biological laboratories
20 Feb, 2020. We are currently looking for an ambitious, highly motivated Postdoc with a good background in AI and an interest in automation with robotics in the field of life science, to join the research group of Assoc. Prof. Ola Spjuth (group website ...
Ola Spjuth presenting at SciLifeLab Chemical Biology Seminar Series
6 Feb, 2020. On Feb 6th 2020, Ola Spjuth held a presentation at Karolinska Institutet, Stockholm in the SciLifeLab Chemical Biology Seminar Series. Approx 50 people attended to this event organized primarily by Jordi Carreras Puigvert. The title of the ...
4 posters at the 10th Pharmaceutical Profiling Symposium
30 Jan, 2020. Our research group presented 4 posters at the 10th Pharmaceutical Profiling Symposium at Uppsala University, on January 30th, 2020. It was a very nice event with 150 registered participants, and talk from varying areas of profiling. Poster ...
3 Dec, 2019. Today, Laeeq Ahmed who is affiliated with the group successfully defended his thesis, titled: “Scalable Analysis of Large Datasets in Life Sciences“ We congratulate Laeeq for his success and wish him well in his future career! ...
Ola Spjuth presenting at Swedish e-Science Academy 2019
16 Oct, 2019. Ola Spjuth gave an invited talk at the conference Swedish e-Science Adademy 2019 in Lund, Sweden on 16 October 2019. The title of the talk was: Towards Automated AI-guided Drug Discovery Labs. Abstract High-content microscopy in automated ...
10 Oct, 2019. Today, Marco Capuccini from the group successfully defended his thesis, titled: “Enabling Scalable Data Analysis on Cloud Resources with Applications in Life Science“ CONGRATULATIONS MARCO! Supervisor: Assoc Prof. Ola Spjuth, ...
Open position: PhD Project in Cell Biology with a focus on Intelligent Automation
7 Oct, 2019. We are looking for an ambitious, highly motivated PhD student with a good background in cell biology as well as interest in molecular biology, high-throughput screening, automation and bioinformatics. The successful candidate will join an i ...
Ola Spjuth presenting at COPA 2019
10 Sep, 2019. Ola Spjuth presented two accepted papers at the 8th Symposium on Conformal and Probabilistic Prediction with Applications in Varna, Bulgaria on 9-11 sept 2019. The two papers below are now published in Proceedings of Machine Learning Resea ...
Group Retreat at Krusenberg Mansion
28 Aug, 2019. On August 27-28, our research group was on a retreat to Krusenberg Mansion, where we had good presentations and discussed planning and strategies on research and education activities in the group. In the evening the social program involved ...
Two papers accepted for COPA2019 and published in PMLR
20 Aug, 2019. We are very proud to announce that we this year had 2 papers accepted to the 8th Symposium on Conformal and Probabilistic Prediction with Applications! Ola Spjuth will present the papers in Golden Sands, Bulgaria on 9-11 sept 2019. Paper ...
2 Open positions: PhD student and Lecturer; focus on AI/machine learning on large-scale data
4 Jul, 2019. Our research group has 2 open positions: One PhD position and one Lecturer position. Deadline for both applications is 2019-08-12. PhD Position Our group is participating in the HASTE project (Hierarchical Analysis of Temporal and Spatial ...
Ola Spjuth presented at SLAS Europe 2019
28 Jun, 2019. Ola Spjuth presented on the SLAS Europe 2019 conference, with the title of the presentation: “Building an informatics solution to sustain AI-guided cell profiling with high-content microscopy imaging“ Abstract High-content micr ...
SciPipe workflow tool published in GigaScience and CiSe
25 May, 2019. A few weeks ago the workflow tool we have developed and used in the group, SciPipe, was published in Gigascience. This article quite comprehensively summarizes our lessons learned in scientific workflow usage and design over the last coup ...
Ola Spjuth presented at Data Innovation Summit 2019
15 Mar, 2019. Ola Spjuth presented on the Data Innovation Summit 2019 conference, with the title of the presentation: “Automating the process of continuously prioritising data, updating and deploying AI models in a robotised lab for drug discovery ...
15 Nov, 2018. Group leader Ola Spjuth received a 3 MSEK grant from the FORMAS Future Research Leaders call in 2018, for a project with the title: Exploring toxicity mechanisms for environmental contaminants using an AI-controlled automated laboratory As ...
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 ...
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 ...
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 ...
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 ...
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 ...
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! ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 “ ...
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 ...