The course "High Performance Computing (HPC) for genomic applications" is organized for the D-BSSE researchers (including PhD and Master students) by the Scientific IT Services. It will be run in this edition in a classroom mode.
Wednesday, December 13th 2023, 9:30-17:00
BSS F 10.1
The main goal of the course is to increase IT competences of researchers and encourage them to use Euler cluster for bioinformatic analyses: independently or together with a bioinformatician in a co-analysis mode. The participants are expected to work on own laptops, using a terminal to connect to the cluster. After the course there are planned time slots, when the participants can discuss or work on solutions for their own data analysis issues with the instructors.
This is the basic, one-day course, which enables participants to take part in the advanced course on workflows and advanced aspects of the bioinformatics on the cluster. It will be announced later, in spring/summer 2024.
The modules of the course are:
As part of the ETH Zurich Data Stewardship Network, we are excited to launch a new seminar series on "Current Topics in Research Data Management and Data Stewardship". The first seminar will take place on Thursday, 7th December 2023 from 15:00 to 16:00. In this seminar, Swen Vermeul from ETH Zurich Scientific IT Services will talk about Graph Databases and why you need them.
Abstract: Traditional relational databases are – despite their name – surprisingly bad when it comes to relations. Storing data is easy as long as the data looks like a table. Unfortunately, in real life, data is often structured and rarely fits into a table. This is where graph databases might become handy, especially when not only data points are important but also relationships between these data points. In this talk I will present you some concepts of noSQL databases, the differences between RDF Triplestores and Labeled Property Graphs as well as the GraphQL API, which makes it easy to get exactly the data you want.
The seminar will be held in a hybrid form with the on-site part taking place in the ETH Main Building in room ETHBIB Kursraum HG J 29.7. As the room has limited capacity, please fill in the registration form if you plan to attend in person. You can also participate in the seminar online via Zoom: https://ethz.zoom.us/j/66297798684 (no registration required).
Please adress any questions concerning the new RDM seminar series by e-mail to Agnieszka Ilnicka (firstname.lastname@example.org).
Two new calls from the Open Research Data (ORD) Programme of the ETH Domain have been launched:
These calls offer financial support for projects related to ORD practices. Further information and the guidelines can be found on the website of the ETH Board.
The aim of this seminar series is to foster the exchange within the EnhanceR network and broaden the network to additional national (and possibly international) Research IT units in the future.
Additional information regarding the iterations, topics of talks and the registration can be found here: https://www.enhancer.ch/seminar.
Interested in joining us on the journey to support personalized medicine for research?
We are hiring - looking for an IT solution engineer.
Scientific Computing in Practice lecture series at Aalto University in collaboration with Code Refinery offer a free workshop to introduce tools for scientific computing with Python. The course consists of four online hands-on sessions 3h each.
The course is open to the world and fully online.
For more details read here.
We have recently announced a four-day course to give a hands-on introduction to writing fast(er) code in Python.
We plan to hold this course on-site at ETH Zurich (OCT E34 & E36) on:
This course will introduce participants to various techniques and tools to help them tackle performance issues when writing Python code. We will discuss tools for codes running on local computers as well as on high-performance-computing clusters.
The course requires some previous Python experience and is not an introduction to Python. It will be suited for people who can answer the following questions with "yes":
For more information about the course read here.
We have received an overwhelming interest in the course, which was filled within a few days.
The openBIS User Group Meeting 2023 will take place in Zurich on 12-14 September 2023.
All information can be found on the openBIS website.
Please note that the workshops on day 2 and day 3 have limited number of places available, which are assigned on a first come first served basis.
Would you like to know what services and infrastructures are available at ETH Zurich for handling of FAIR Research Data?
Join the next online-presentation of the Open Science Working Group and learn more about the development of Research Data Management at ETH Zurich. All information about the lunchtime event on
Tuesday, 5 September, 12:30 to 13:30
The ETH Library and the ETH Scientific IT Services run a series of workshops covering different topics related to Research Data Management (RDM). The workshops will be held mostly online, between end of September and end of November 2023. For more details see here.
The ETH Open Science working group is organizing two information events on the topic of research data management at ETH Zurich. The events will provide an insight into the new Research Data Management Guidelines (RDM Guidelines), the development of research data management at ETH and the support services and data infrastructures available to researchers.
The first event is aimed at ETH members in the central services and will take place online on Monday 24 July 2023 from 11:00 to 12:00. Further details and registration information here.
The second event is aimed at ETH researchers and will take place online on Thursday, 27 July 2023 from 11:00 to 12:00. Further details and registration information here.
The Leonhard Med team is pleased to announce the 1st Leonhard Med User Meeting that will take place on July 6th, 2023, in person at the OCTAVO offices in Zurich. The users will have the opportunity to exchange knowledge, give personal feedback and express their wishes on the service. All LeoMed users are invited and were informed via email.
The Expert Group Services and Infrastructure of the ETH ORD Program is organizing a full-day workshop on technical interoperability between ORD services and repositories in the ETH Domain. The workshop will take place on Thursday, June 29, at the University of Bern. For further information and registration, please visit the workshop website.
SIS continues excellent collaboration with ETH Library and presents at the upcoming ETH Research Data Management Summer School 2023 that will take place 12 to 16 June 2023.
SIS experts will share insights on Research Data Management with openBIS, version control with Git and secure handling on sensitive data with Leonhard Med.
The Leonhard Med Coffee Hour is a monthly informal online gathering where LeoMed users can chat with members of the LeoMed team. The first event will take place on June 12, 2023.
Who should join:
LeoMed users can find more information here.
The ETH Domain ORD Program has launched a call to target the limited interoperability between Electronic Lab Notebooks (ELNs). With this call for proposals, the ORD Program will fund one or more projects that aim to improve the interoperability between ELN systems in the ETH Domain.
The call is advertised on the website of the ETH Board and the deadline for proposal submission is on 31 August 2023 at 17:00.
We are seeking a Scientific Computing Expert to strengthen our team of experts to support researchers in finding, setting up and using the right tools and compute resources for their scientific work.
Please check our job ad.
We released openBIS 20.10.6. It brings improvements to UI navigation and data import/export, among other new features and bug fixes. For more, see the release notes.
The National Centres of Competence in Research (NCCRs) are organizing a series of three events on Open Science and Open Research Data (ORD), with presentations and workshops by experts and researchers who develop methods for practicing various aspects of ORD.
Scientific IT Services will contribute to the event in Zurich with one plenary talk and three workshops, which cover the topics of research data management, working with sensitive data and code management with git.
For more information read here.
Scientific IT services participates at the forum for young academics of the Deutsche Gesellschaft für Materialkunde (German Society for material science) in Kassel, Germany under the umbrella of the openRDM.eu project.
Rostyslav Kuzyakiv (SIS Research Data Management Expert) contributes with two workshops about Active Research Data Management and openBIS ELN LIMS training session for students and young scientists.
You are a professional web developer and want to work in a scientific environment?
Please check our job ad.
We are pleased to announce a four-day course to give a hands-on introduction to the field of machine learning using Python.
The course will take place on on Thu 16th, Fri 17th, Thu 23rd and Fri 24th March 2023.
The course is fully booked and we plan to offer the workshop again early 2024.
For more information about the course
and how to apply
The new extension Euler VIII has passed all acceptance tests and is now fully operational. Euler VIII features:
All nodes are open to user jobs through the queueing system.
We offer now a RSS feed at https://sis.id.ethz.ch/feed/rss.xml which includes the news from this page.
The most relevant new features and bug fixes of this new release are:
The full list of changes is available here.
This version can be downloaded from the production releases page of our wiki.
Yesterday, the EnhanceR association held its first symposium in Berne. The Swiss science IT community met to better get to know each other and share work they have been doing as well as issues they were facing. We had good discussions and exchange. To be repeated...
The next extension of the Euler HPC cluster, called Euler VIII, has been delivered and racked by Dalco. It contains 192 nodes with 128 AMD Epyc cores each. Now the company is working on passing all the acceptance tests so Euler VIII can be handed over to the HPC team who will put it in production.
A consortium including PSI, Empa and ETH Zurich, led by Dr. Giovanni Pizzi, Group leader of the “Materials Software and Data” group at PSI, has won funding of almost CHF1.3 million for a three-year project dubbed PREMISE: “Open and reproducible materials science research.” The PREMISE project aims to establish, promote and facilitate the adoption of ORD practices that adhere to FAIR data principles in the field of materials science.
In addition to Dr. Pizzi, the consortium consists of Dr. Carlo Pignedoli, deputy group leader of the “Atomistic simulations group” at Empa; Dr. Corsin Battaglia, laboratory head of the “Materials for Energy Conversion lab” at Empa; Dr. Bernd Rinn, section head at the ID Scientific IT Services group at ETH Zurich; Dr. Caterina Barillari, RDM service manager in the ID Scientific IT Services group at ETH Zurich; Dr. Henry Lütcke, scientific computing lead in the ID Scientific IT Services group at ETH Zurich and Dr. Peter Kraus, scientist in the “Materials for Energy Conversion lab” at Empa.
Further information on the project is available here.
Scientists nowadays collect ever larger amounts of data that have to be stored, interpreted and shared.
Furthermore, new guidelines and policies regarding data management are regularly issued by funding agencies, journals or academic institutions. As a result, successful research data management has become both a key skill and a major challenge for many scientists.
In collaboration with ETH Library, we participate in a workshop series of eight consecutive workshops focusing on the various elements of research data management and the research data life cycle.
The first workshop on Research Data Management Basics will start on September 28, 2022. Subsequent workshops will run throughout October and November.
Further information and registration is available here.
Professional research data management (RDM) is a key factor for excellent research and an integral component of good scientific practice. In recent months, the Open Science working group of ETH Zurich – with the active involvement of the ETH research community – has drafted guidelines for RDM at ETH Zurich and systematically linked them with the Integrity Guidelines. The working group is drawn from different ETH divisions, among them the Research Commission, ETH Library and SIS. The new guidelines for research data management have been approved by the ETH Executive Board in June and came into effect on July 1. SIS supports researchers in the implementation of the new guidelines by offering different RDM services and a secure data and IT platform for management and processing of confidential and strictly confidential Research Data (Leonhard Med).
SIS was involved teaching data management and reproducible data analysis. We also contributed several workshops:
ITS SIS is organizing a conference track at the Applied Machine Learning Days 2022 (AMLD 2022) on the topic Academic Support & Scientific Services in AI.
The purpose of this track is to bring together domain scientists and AI experts who work collaboratively. These scientists and experts will share their experiences on the benefits and challenges of such "AI collaborations".
We have speakers from SDSC, Google, ScopeM, TCC/UniZH, etc. You can find a detailed description of our track, including speakers and agenda of the track, here At the end of the track, there will be a panel discussion for further exchange. We are looking forward to a diverse and stimulating session.
AMLD 2022 will take place from March 28-30, 2022, in Lausanne. Our track will be held on the 30th of March from 11:00-17:00. If you have time and interest in this topic, we would be delighted to see you at our track.
The latest version of the AI-based AlphaFold has been recognized as a solution to the 50-year-old grand challenge in predicting the protein 3D folding structure by its amino acid sequence. To facilitate the use of AlphaFold2 for the ETH research community, Scientific IT Services (SIS) provide its Python package and databases required for running AlphaFold2 on the HPC Euler cluster. In this online event, we would like to present you the usage of AlphaFold2 on Euler and examples of applications.
Date: Monday 21 March 2022 at 10:00-11:00
Zoom link: https://ethz.zoom.us/j/64638964004
We are looking forward to seeing you at the event.
For questions, please contact email@example.com.
The BioMedIT project was launched in 2017 as part of the SPHN initiative, linking secure computing infrastructures in Basel, Lausanne and Zurich. At the moment, the project provides essential IT and data management services to over 60 national and international projects. Furthermore, to highlight this success, the project launched its website today.
The overall goal of personalized health research is to optimize disease diagnostics, prevention, and treatment based on patient characteristics (molecular, clinical and phenotypic). However, this is possible only if a critical mass of datasets, typically scattered across several healthcare institutions, can be analyzed efficiently and consistently.
BioMedIT makes it easier to reach this critical mass by offering an easy and secure way to conduct large multi-site projects. It builds on and integrates results from parallel initiatives around data interoperability at the national level.
For more details of BioMedIT, including success stories and organizational structure, please refer to the news item (English, German and French (links)). For more information about BioMedIT activities in ETH Zurich, please get in touch with the Leonhard Med team.
The ETH-Board together with the six ETH-Domain institutions have allocated up to CHF 10 million till the end of 2024 as a measure to launch an open research data (ORD) practices funding scheme. ORD includes code, computing environments, tools/hardware, wetware, educational resources and generally any information that is necessary to do research. The programme’s overall goal is to promote ORD practices and infrastructures across the ETH-Domain and stimulate a wider implementation of good ORD practices.
The scheme consists of three tracks for funding projects to contribute to ongoing, explore new, and establish standards/processes of ORD practices; these three distinct project types are described on the website of the ETH Domain. Please note that specific budgeting requirements, funding and regulations for in-kind or in-cash contributions apply for ETH Zurich applicants (see call details).
Open calls for Field-Specific Actions (Measure 1):
The first call for “Explore” projects (deadline set for 14 April 2022) and the call for “Establish” preproposals (deadline 1 May 2022) have been closed. The next call for “Contribute” projects will be advertised on the Website of the ETH-Board soon.
We are pleased to announce a three-day course to give a hands-on introduction to write fast(er) code in Python.
Because of the COVID-19 safety regulations at ETH Zurich this course edition is being held entirely online on Zoom at the following days and times:
The course requires some previous Python experience and will be suited for you if you can answer the following quesions with "yes":
The course will give you an introduction into different techniques and tools which help you to tackle performance issues when writing Python code either on your local computer and/or on a high-performance computing cluster.
This course is not an introduction to Python and does not offer a deep-dive into the presented topics. Instead, we try to raise awareness of existing solutions and to teach best-practices so that participants can acquire the basic skills needed to tackle performance related programming problems on their own.
For more information about the course and how to apply read here.
We would like to invite you to our short lecture on scientific computing with computational notebooks taking place on
17 November 2021 at 15:15-15:30
Please find the Zoom link to join the lecture and more information here.
We would like to invite you to join our online workshop on Getting Started with the Scientific Cluster taking place on
Thursday 14 October 2021, 10:00-15:00.
For more information and registration, click here
We are pleased to announce the openBIS User Group Meeting 2021. The event will take place online from 27th to 30th September 2021.
The first day there will be a few talks from users and a round table of discussion. The following days we will offer several workshops on different topics.
The first day is open to anyone, but registration is mandatory. The workshops have limited places available.
For more info and registrations check the event website.
We are pleased to announce a four-day course in Parallel Programming with MPI/OpenMP being held on
August 23 - 26, 2021.
For more details read here.
We offer the openBIS ELN and LIMS Training over Zoom. The training has two parts:
For more information and registration, click here
The openBIS team is proud to officially introduce openBIS 20.10.0 RC (Release Candidate). This release has a focus not only on introducing new features, but also on refining existing components.
We would like to invite you to a webinar where we will introduce the major new features of this latest openBIS release. You will also have the chance to talk and ask questions to our openBIS developers. The webinar will take place on Thursday 12.11.2020 at 14:00-15:30.
A video recording of the webinar is available here.
We offer a two day course introducing Python to members of C2SM.
The course introduces the Python programming language to students and researchers having basic programming skill in another programming language already.
This course is suited for you if:
The course will be to fast if you never programmed before.
The course will be given on 1st and 2nd of October 2020, 9:00-13:00 via zoom.
In case of further questions please contact firstname.lastname@example.org.
Did you miss the Leonhard Med Info-Event or would you like to see it again? Take a look at the video recording! Read more here.
The Scientific IT Services of ETH Zurich and LOOP offer an info event for principal investigators and other potential applicants who are preparing research proposals for the current LOOP call.
Contact: Diana Coman Schmid, email@example.com