Category Archives: berkeley lab

2 September 2023
berkeley lab, english, projects, resources

Lamaseries

It’s been a few months since the ChatGPT craze started, and we’re finally seeing some interesting courses and guidelines, particularly for coding, where I found the whole thing quite impressive.

https://static.tvtropes.org/pmwiki/pub/images/llama_loogie_tintin.jpg

Ad hoc use of LLaMa

Here’s a few that can be of interest, potentially growing over time (this is mostly a notes to self.)

Plus – things are getting really crazy: Large language models encode clinical knowledge (Nature, Google Research.)

 

17 August 2023
berkeley lab, english, projects, resources, science, science life

Updates on AI for big science

There’s a lot of things happening on the front of AI for Big Science (AI for large scale facilities, such as synchrotrons.)

The recently published DOE report in AI for Science, Energy, and Security Report provides interesting insights, and a much-needed update to the AI for Science Report of 2020.

Computing Facilities are upgrading to provide scientists the tools to engage with the latest advances in machine learning. I recently visited NERSC’s Perlmutter supercomputer, and it is LOADED with GPU for AI training.

A rack of Tesla A100 from the Perlmutter supercomputer at NERSC/Berkeley Lab

Meanwhile, companies with large computing capabilities are making interesting forays in using AI for science, for instance Meta, which is developing OpenCatalyst in collaboration with Carnegie-Mellon University, where the goal is to create AI models to speed up the study of catalysts, which are generally very computer-intensive (see the Berkeley Lab Materials Project.) Now the cool part is to verify these results using x-ray diffraction at a synchrotron facilities. Something a little similar happened with AlphaFold where newly derived structure may need to be tested with x-rays at the Advanced Light Source: Deep-Learning AI Program Accurately Predicts Key Rotavirus Protein Fold (ALS News)

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31 July 2023
berkeley lab, english, resources, science

Institutional Open Data

Things are moving in terms of Open Data! The Department of Energy has just released an update to it Public Access Plan (initially published in 2014), and embracing the use of persistent identifiers for papers and data, to promote the FAIR principles (Findability, Accessibility, Interoperability, and Reusability of data and metadata.)

Mariposa Lillies, from Alexis Madrigal of the Oakland Garden Club

And let me insist on the last bit:

Data without metadata is mostly useless

At the time where Twitter was a nice place to share thoughts and disseminate bite-sized knowledge, I thought the Twitter posts/URL were something akin to Digital Object Identifiers – you could post an image with caption, and share the link on your blog or with anyone (now Twitter doesn’t allow to share those so easily.) Zenodo allows you to creat actual DOI for your data (data will include your ORCID and metadata.), albeit not as user-friendly – and to some extent, github works the same way (the visualization and graphical content is not the best)

At Berkeley Lab, the Office of Research Compliance has updated its guideline, providing excellent resources to build a Data Management Plan.

11 July 2023
berkeley lab, english, projects, resources, science life

Out Of Many

Last week I was lucky to meet with Vanessa Chan, the Chief Commercialization Officer for the Department of Energy and Director of the Office of Technology Transitions. She wanted to hear what kind of hurdles when it comes to start a company (hint: a lot.) I told her that a major, overlooked issue is that you generally to be a permanent resident to start at company in the US, whereas two-thirds of postdocs are foreign nationals and on visas. There are ways to get around the requirement (such as Unshackled), but it’s a little sad not more is done to provide support to those willing and able (plus – it is a well-known trope that many US companies are founded by foreign nationals, what I tend to believe is among what sets California apart from other states and other countries, where entrepreneurship doesn’t flourish as much as expected despite many efforts)

Conversation with Vanessa Chan

29 March 2023
art, art & science, berkeley lab, english, projects, resources, science life

SFMOMA x Berkeley Lab: Hybrid forms

Yesterday I invited Tanya Zimbardo from the San Francisco Museum of Modern Art to give a talk at Berkeley Lab (details about the even can be found here: Hybrid Forms: Connecting Art and Science)

Tanya Zimbardo (SFMONA) at Berkeley Lab

It was quite interesting to hear her perspective on a topic which is close to my heart, and happy to hear many references to Rafael Lozano-Hemmer, who currently has the Techs-Mechs exhibition running at the Gray Area, but also quite surprising not hear anything about Jim Campbell (whose art glows atop the Salesforce building “Eye of Sauron”) or the work of Illuminate.

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10 February 2023
berkeley lab, english, resources, science, science life

SMART & TGROW

Acronyms, I like acronyms!

Here are two resources that I found useful for (1) supervising researchers (SMART) and (2) mentoring scientists (TGROW)

SMART

(this is an excerpt from the Virtual Remote Mentor Guide -DOE-SC-WDTS Programs)
SMART is an acronym for a framework to help guide goal setting. It is intended to ensure that goals are planned, clear, trackable, and reachable. With SMART goals, you are more likely to achieve the goal efficiently and effectively. Below is an overview of the framework to establish SMART goals.

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6 December 2022
berkeley lab, english, mood, resources, science life

1000 days

Today is the thousandth day since the start of the pandemic, and we still haven’t figured out how to hold efficient meetings online.Here’s a useful resource:

A practical guide to Remote & Hybrid Communications – Berkeley Executive Education
https://drive.google.com/file/d/14ztjFkkKQGHK-HOtebUOtu-Lpa3DanVt/view

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29 November 2022
berkeley lab, english, projects, science

Using machine learning to achieve diffraction-limited performance with x-rays deformable mirrors

In a our last paper, we present the use of machine learning to get the most of x-ray adaptive optics – and it works like magic! This was a great work accomplished by Gautam Gunjala, a grad student from UC Berkeley under a SCGSR grant, together with our wonderful colleagues from the Advanced Photon Source.

X-ray adaptive mirrors are very nice, because they allow to correct the shape of x-ray beams, when the beam gets distorted by mirror deformation or misalignment. That’s why we want to use them in the latest generation of synchrotron light source such as ALS-U or APS-U.

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22 November 2022
berkeley lab, english, science, science life

ALS-U CD-3

The Advanced Light Source upgrade project has received the Critical Decision 3, the very last step before we start building the facility – a $590M project for the US Department of Energy.

This is a great news for the facility, which will become the brightest soft x-ray light source in the world. I have worked on this project over the last five years, designing and simulating the new feature beamlines and developing new technologies to ensure optimal performance.

Berkeley Lab news center: Advanced Light Source Upgrade Approved to Start Construction

“Wavefront Preservation in Soft X-Ray Beamlines for the Advanced Light Source Upgrade.”
Antoine Wojdyla & Kenneth A. Goldberg
Synchrotron Radiation News, 34(6), 21–26 (2021).
https://doi.org/10.1080/08940886.2021.2022398

12 November 2022
berkeley lab, english, resources, science, science life

Penn State University (Fall 2022)

I had a great time at Penn State University, where I was positively impressed by the facilities and the people!

I mainly visited the Material Research Institute and the department of Astronomy and Astrophysics, where they are developing x-ray adaptive optics for space application together with NASA, for the Lynx project.

Millennium Science Center, Penn State University (November 2022)

Thanks Susan Trolier-McKinstry for hosting me!

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