Cern News

CERN software to become central hub for EU research (Image: Zenodo)

What is the link between particle physics, the study of biodiversity and historical linguistics? The thirst for knowledge? Yes, but also the tool researchers are using to store all their findings and make them available to their peers: Zenodo. For more than ten years, this CERN-born data repository has been evolving to store scientific data for ever more research communities and to adapt to the needs of more scientific disciplines. Notably, it was a key player in the COVID-19 response, providing a platform for researchers to efficiently share results, data sets and software to help the international scientific community respond to the pandemic. Today, it is used by more than 8000 research organisations worldwide.

This success story is about to take an even more ambitious turn with a new project: HORIZON-ZEN. Since its inception in June 2023, it has become the latest in a series of projects funded by the European Union to make the data collected by European research more findable, accessible, interoperable and reusable (FAIR). Since 2021, making research data as FAIR as possible has become a requirement for all projects funded by the European Commission.

What does it mean to make data FAIR in practice? Today, this is still difficult for researchers to navigate, because FAIR are generic principles rather than verifiable criteria. “With HORIZON-ZEN, we are striving to make being FAIR simpler and more streamlined for researchers, and we are working with scientific communities to tailor Zenodo for their specific domain,” explains Lars Holm Nielsen, Section Leader in Open Science Repositories in CERN’s IT department.

As part of the project, Zenodo will be updated with a bespoke “European Commission” user interface. (Image: CERN)

Zenodo was born out of the need for a simple, easy-to-use storage solution for all types of research output: papers, theses, presentations, protocols, images, videos, data sets, software, etc. Generally, Zenodo is the ideal tool for researchers without a dedicated research infrastructure, for communities with a large network of institutes or for small institutes that have the necessary knowledge but not the tools. “Zenodo is the brainchild of the EU's open science policy. The European Commission has high hopes for this service, which could eventually become one of the EU's main repositories for research data,” Nielsen continues.

To make this possible, Nielsen and his team are putting a special, community-driven effort into the user experience, making it is easy for communities to customise their space, curate their content and build their online domain. “We are taking advantage of the 10 000 communities and the 300 currently running European-funded projects using Zenodo to co-design our tools. We encourage scientific communities to get a tailor-made Zenodo experience by becoming early adopters.”

Zenodo owes its success to the scientific community’s confidence in CERN, to ten years of continuous support by the European Commission and to the remarkable services provided by the tool. Above all, it is the result of the hard work of a small team at CERN who are eager to maximise the impact of CERN technologies.

The HORIZON-ZEN project is funded by the European Union under Grant Agreement No. 101122956.

 

 

ndinmore Tue, 01/23/2024 - 09:49 Byline Antoine Le Gall Publication Date Tue, 01/23/2024 - 09:39

BioDynaMo: cutting-edge software helps battle cancer

Choosing the right cancer treatment is a massive undertaking involving multiple stages, high experimental complexity and significant costs. Currently, two main methods are used to find the best possible treatment solutions: in vitro testing and clinical trials. However, predicting the drug effects on each individual patient remains the Holy Grail of personalised medicine.

Born from CERN openlab in the CERN IT department, BioDynaMo is an innovative tool for “in silico” testing, i.e. experimentation carried out on a computer. Based on mathematical models, it creates and runs complex 3D computer simulations that help understand cancer progression and identify the most effective treatment strategies for specific tumour cases.

In a recent scientific publication, scientists affiliated with CERN, the Technical University of Munich and the University of Texas at Austin demonstrated the significant potential of advancing medical therapy with the help of BioDynaMo. The model successfully replicates medical data on recorded tumour growth and the effects of two anti-cancer drugs, Doxorubicin and Trastuzumab. By fitting the BioDynaMo models to the available pre-clinical data, scientists proved the platform’s ability to simulate different levels of efficacy of various drugs, treatment combinations and dosage regimens.

BioDynaMo is an open source project that strives to provide the most efficient and performant simulation platform for agent-based models. It accommodates a diverse range of use cases and can address research questions in oncology, neuroscience, epidemiology and many more disciplines. With its ability to simulate almost two billion agents (or cells), BioDynaMo is a powerful tool for analysing many different complex systems. Since 2015, BioDynaMo's consortium of scientists has been working on developing and optimising the engine, improving its performance and usability. For more information, click here.

The BioDynaMo project is funded with the support of CERN’s budget for knowledge transfer for the benefit of medical applications and of the CERN and Society Foundation. Find out how you can support the BioDynaMo project here.

ndinmore Tue, 01/16/2024 - 11:54 Byline Marina Banjac Publication Date Tue, 01/16/2024 - 11:43

CERN Alumni Third Collisions: A confluence of reconnection, networking and celebration  

"Great stories of entrepreneurship! It was amazing to see the impact that CERN alumni are making in society." These are the words of a CERN alumni who took part in the Second Collisions event, in 2021. These sentiments echo the anticipation surrounding the upcoming Third Collisions event, taking place at CERN from 9 to 11 February.

In less than a month, CERN will play host to several hundred alumni, marking the third reunion of this network, now entering its seventh year of existence. The event promises a rich tapestry of experiences, blending insightful talks, stimulating panels, and the chance to reconnect with former colleagues. The focus of the talks and panels extends beyond the scientific realm, delving into pressing topics like climate change, artificial intelligence, and quantum computing. The event serves as a nexus for networking, providing opportunities for alumni to reconnect and engage with members of the CERN community.

A notable addition to this year's programme is the inaugural jobs fair, bringing together companies and EIROforum organisations actively seeking individuals with skills cultivated at CERN. CERN Alumni companies will also feature, as will CERN teams such as Knowledge Transfer, CERN Courier, and the CERN & Society Foundation, amongst others. Many companies will be in place, as of the afternoon of Thursday, 8 February, in the Main Building, and will eagerly welcome those at CERN contemplating their next professional venture.

The Third Collisions aren't just about work; they encompass a spectrum of events, sparking CERN nostalgia, including a welcome reception, gala dinner, and multiple coffee breaks that facilitate informal networking. The agenda also boasts diverse entertainment options, ranging from a ski outing to a MusiClub alumni DJ set and the screening of "Almost Nothing", followed by a Q&A with one of the directors. Fitness activities are also on the menu, ensuring a well-rounded experience for all participants.

The event's detailed programme, list of speakers, and additional information can be accessed here.

To facilitate participation, a small financial contribution is requested, ensuring the smooth execution of this grand event. For the first time, participants are welcome to bring a plus one (over 18s only), enhancing the sense of community and celebration.

Additionally, the organising committee is seeking volunteers to contribute to the event's success. Those willing to lend a helping hand will have their registration fees waived, further emphasising the collaborative spirit that defines the CERN and CERN Alumni communities. Please contact alumni.relations@cern.ch for more information.

Join us at CERN Alumni Third Collisions, which promise to be an extraordinary blend of knowledge exchange, professional networking, and celebration, reinforcing the impact of CERN alumni on society and echoing the continuous legacy of excellence set by CERN and its remarkable alumni.

anschaef Tue, 01/16/2024 - 10:37 Byline CERN Alumni programme Publication Date Tue, 01/16/2024 - 10:34

Computer Security: Hits are coming closer

Like it or not, the cyber realm is unfortunately developing alongside the physical world. While in the real world, conflicts tragically dominate world politics, the usual commercial cyber-attackers have increased their attacks, too. And, unlike in the past, the research and education (R&E) sector is no longer spared.

Until recently, universities had been attacked only very occasionally. One of the last in this sad line-up was the University of Michigan. But the last year has also seen major attacks against accelerators and telescopes ─ as collateral damage and as the attackers’ main focus, respectively. What we feared in the past has become reality: where there is operational value, there is a business opportunity for malicious evildoers to extract money ─ and this applies to the R&E community as well. To “ransom” the operator, threaten operations, stop production and cause damage.

Over the past 12 months, the CERN Computer Security team has tirelessly helped dozens of universities worldwide to protect themselves against such “ransomware” attacks (see our monthly security reports) and improve their defences, as well as providing training, tipping them off to imminent danger where our threat intel permits and assisting them in incident response when it was too late and damage had been done. Similarly, the base question is not “if” but “when” CERN will be subject to a ransomware attack. The three mantras of ransomware defence are “Don’t get it”, “Don’t pay” and have all-encompassing, complete and thoroughly tested back-ups in place. While CERN has taken a firm position on the second mantra (incidentally, governments are increasingly prohibiting ransom payments), and the IT department, in collaboration with many stakeholders in the Organization, is hard at work on the third, the first mantra – raising our defences – is the hardest one. Many projects are already under way and we’re not done yet:

• 2024 will see an even more all-encompassing roll-out of 2-factor protection, in particular to our user community and to holders of so-called “secondary” accounts. It will eventually also cover LXPLUS and the CERN Windows terminal servers.
• The “new” anti-malware solution will finally be deployed to all CERN/centrally managed Windows PCs and we will investigate whether this protective means can also be forced onto any other Windows laptop or Macbook purchased and owned by the Organization.
• Vulnerability scanning and penetration testing against CERN’s internet presence is currently being tendered and will start in early 2024 (the owners of vulnerable websites and web servers may possibly be required to contribute to the cost).
• Together with HR’s Learning and Development group, we will expand CERN’s training catalogue and offer dedicated hands-on courses on secure programming and software development, as well as IT operations.
• In parallel, Gitlab security scanning may make it into your pipelines and into your choice of virtual machines and containers in order to reduce the risk through the “software supply chain”.
• Our Security Operations Centre will extend its remit to cover even more data sources, enabling us to monitor more network segments than ever before, as well as our main cloud-based services (such as Google and Microsoft).
• Finally, CERN recently concluded an external audit on “cyber security” and its findings and resulting recommendations will be addressed in the course of 2024 (more on that in a future Bulletin article).

In any case, ransomware hits are coming closer. Unlike some of our unfortunate partner universities and some astronomy experiments and particle accelerators, CERN has not been hit yet. Yet! And we hope to keep it that way. Cybersecurity is a permanent marathon: our work will never be done. But for this race, we appreciate (and need!) your help in securing the Organization. As “sec_irty” is not complete without “u”!!! Let’s have a (more) peaceful 2024.

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Do you want to learn more about computer security incidents and issues at CERN? Follow our Monthly Report. For further information, questions or help, check our website or contact us at Computer.Security@cern.ch.

In case you missed it in December, the talk "CERN Computer Security: Abuse, Blunder and Fun" will be repeated on 30 January at 11 h in the Council Chamber. More information on Indico: https://indico.cern.ch/event/1365440/ anschaef Mon, 01/15/2024 - 11:48 Byline Computer Security team Publication Date Mon, 01/15/2024 - 11:45

LHCb experiment releases all of its Run 1 proton–proton data

At the end of December 2023, the LHCb experiment released all its data from Run 1 of the Large Hadron Collider. This data, collected by the experiment in 2011 and 2012, contains approximately 800 terabytes of information obtained from proton–proton collisions. The data has been made available in a pre-filtered format, suitable for a wide range of physics studies for research and education purposes. 

LHCb data across Runs 1 and 2 has already been used for over 700 scientific publications, including numerous significant findings. All results from the collaboration have already been made publicly accessible in open-access papers and the numerical results from the graphs can be consulted in the HEPData database. With the new release, the data used by the researchers to produce these results is now accessible. The data has been released in the framework of CERN’s Open Data Policy, which reflects values that have been enshrined in the CERN Convention for more than sixty years and applies to all of CERN’s activities.

The collaboration has pre-processed the data by reconstructing experimental signatures, such as the trajectories of charged particles, from the raw information delivered by the complex detector system. The data is filtered, classified according to a large number of processes and decays, and made available in the same format that is used internally by LHCb physicists. The data can be downloaded from the CERN Open Data portal.

To aid the user’s understanding, the samples come with extensive documentation and metadata, as well as a glossary explaining several hundred specialised terms used in the pre-processing. The data can be analysed using dedicated LHCb algorithms, which are available as open-source software.

All data sets have digital identifiers (DOIs) for reference and citation. The experiment also welcomes feedback on how the data is used and invites users to discuss and post questions in the CERN Open Data Forum.

ndinmore Thu, 01/11/2024 - 11:28 Byline LHCb collaboration Publication Date Thu, 01/11/2024 - 11:21