12-digit factor of P2203 has now been found by the project...  |
|
...405866 times - still no sign of any larger factors
|
|
| M Queens 27 additional workunits |
| We have to process some additional workunits. Some returned already. |
|
| Rosetta version 4.23 released for testing |
|
The Rosetta application has been updated to include a protocol named GALigandDock that will be used to screen an ultra-large library of small molecules for drug discovery. Please report any issue in the discussion thread here: https://ralph.bakerlab.org/forum_thread.php?id=892
|
|
| P2203:240000000 wu's (of 10000 trials each equiv.) processed! |
|
Thanks to all the users. Please keep crunching!
|
|
| Update of the results of the last 15 days // Actualización de los resultados de estos últimos 15 días |
Dear volunteers,
Allow me a brief message to update you on how the results are going after 15 more days of simulation.
5 iterations of the algorithm have already been completed. Of the 100 markers that we are using, 89 have already been achieved in the normal range (initially only 77 were). On the other hand, the distance between the average experimental behavior and the model has been reduced by 56.84%.
Several parameters of the algorithm indicate that there is still room for improvement.
We will keep you informed.
All the best,
Jesus.
===================================================
Estimados voluntarios:
Permitidme un breve mensaje para actualizaros cómo van los resultados después de 15 días más de simulación.
Se han completado ya 5 iteraciones del algoritmo. De los 100 marcadores que estamos utilizando, ya se ha conseguido que 89 estén en rango normal (inicialmente solo lo estaban 77). Por otro lado, la distancia entre el comportamiento medio experimental y el modelo se ha reducido un 56.84%.
Varios parámetros del algoritmo nos indican que sigue habiendo margen de mejora.
Os mantendremos informados.
Un saludo,
Jesús.
|
|
| News about Einstein@Home searches for radio and gamma-ray pulsars |
Dear Einstein@Home volunteers, read more |
|
| International Women's Day Challenge on March 8th |
|
Welcome back from Tour de Primes! We're kicking off March with a lightning round single-day challenge! Read on...
The second challenge of the 2023 Series will be on International Women's Day, a global holiday celebrated annually on March 8 as a focal point in the women's rights movement, bringing attention to issues such as gender equality, reproductive rights, and violence and abuse against women. The challenge will be 1-day in duration and offered on the SGS-LLR application, beginning 08 March 15:00 UTC and ending 09 March 15:00 UTC.
To participate in the Challenge, please select only the Sophie Germain Prime Search (LLR) project in your PrimeGrid preferences section.
Nonplussed? Nostalgic? Nihilistic? Nervous? Newly inspired? Join the discussion at https://www.primegrid.com/forum_thread.php?id=10168
|
|
| M Queens 27 has finished |
| The M Queens subproject has finished last weekend. No more workunits are distributed. Now we are analyzing the results which are 8 GB of compressed data. Much thanks for your provided work. |
|
| ATM |
|
Hello GPUGRID!
You‘ve already noticed that a new app called “ATM” has been deployed with some test runs. We are working on its validation and deployment, so expect more jobs to come on this app soon. Let me briefly explain what this new app is about.
The ATM application
The new ATM application stands for Alchemical Transfer Method, a methodology Emilio Gallicchio et al. designed for absolute and relative binding affinity predictions. The ATM method allows us to estimate binding affinities for molecules against a specific protein, measuring the strength at which they bind. This methodology falls under the category of alchemical free energy calculation methods, where unphysical intermediate states are used to estimate the free energy of physical processes (such as protein-ligand binding). The benefits of ATM, when compared with other common free energy prediction methods (like the popular FEP), come from its simplicity, as it can be used with any forcefield and does not require a lot of expertise to make it work properly.
Measuring experimental binding affinities between candidate molecules and the targeted protein is one of the first steps in drug discovery projects, but synthesizing molecules and performing experiments is expensive. Having the capacity to perform computational binding affinity predictions, particularly during drug lead optimization, is extremely beneficial. We are actively working now on testing and validating the ATM method so that we can start applying it to real drug discovery projects as soon as possible. Additionally, since these methods are usually applied to hundreds of molecules, it benefits a lot from the parallelization capabilities of GPUGRID, so if everything goes as expected, this could potentially send lots of work units.
The ATM app is based on Python, similar to the PythonRL application, where we ship it with a specific python environment.
Here are the two main references for the ATM method, for both absolute and relative binding affinity predictions:
Absolute binding free energy estimation with ATM: https://arxiv.org/pdf/2101.07894.pdf
Relative binding free energy estimation with ATM:
https://pubs.acs.org/doi/10.1021/acs.jcim.1c01129
For now we are only able to send jobs to Linux machines but we are hoping to have a Windows version soon.
|
|
| Nebula progress report |
|
Check out our latest newsletter: Final update.
|
|
| Storage problem (again) |
As all of you already know we are constantly struggling with our problematic storage. The University have bought a new one and they planned the moving procedure. The HPC cluster should be moved this Monday (March, 6th), the other resources will follow.
I will reasonably shut down the server when needed, I will tell you when as soon as I know the date. Meanwhile the work generator will be active just a few hours a day, so very few workunits will be available.
Thank you all for your understanding and patience.
|
|
| New N-Body Runs |
Hello everyone,
The following are the new runs for N-Body:
de_nbody_02_27_2023_v182_pal5__data__1
de_nbody_02_27_2023_v182_pal5__data__2
de_nbody_02_27_2023_v182_pal5__data__3
These are our first runs of Palomar 5 with data from SDSS DR17.
Please let me know if there are any issues with these new runs.
Thanks,
Kevin
|
|
| DENIS merchandising on the BOINC web store // Merchandising de DENIS en la tienda web de BOINC |
Dear volunteers,
The Science Commons Initiative has created a store to sell merchandising from BOINC projects to help fund the development of BOINC and the projects as well.
We have given them permission so you can find products with the DENIS logo. 50% of the profits on these products will go to develop BOINC and the other 50% will be donated to support DENIS.
You can see them at https://www.redbubble.com/es/shop/ap/138889661
However, if you have any questions about the products or anything related to the store, you can contact them. We are only responsible for having given permission to use the logo.
All the best,
Jesus.
=================================================
Estimados voluntarios:
La Science Commons Initiative ha creado una tienda para vender merchandising de proyectos BOINC para ayudar a financiar el desarrollo de BOINC y también a los proyectos.
Les hemos dado permiso así que podréis encontrar productos con el logo de DENIS. El 50% de los beneficios en estos productos irán para desarrollar BOINC y el otro 50% lo donarán para apoyar a DENIS.
Podéis verlos en https://www.redbubble.com/es/shop/ap/138889661
No obstante, cualquier duda con los productos o cualquier cosa relacionada con la tienda, podéis poneros en contacto con ellos. Nosotros solo somos responsables de haber dado permiso para utilizar el logo.
Un saludo,
Jesús.
|
|
| BOINC merchandise by the Science Commons Initiative |
Dear participants,
There is a wonderful new beginning started by the Science Commons Initiative. They launched a web store selling BOINC-related merchandise. SiDock@home is already on board :)
We support this idea and hope it will help more people to know about BOINC and get interested in BOINC projects! It will also contribute to the development of BOINC as 50% of the profits will go to the BOINC Development Fund (100% in special cases). Another 50% of the profit will go to the project as a donation.
With best wishes,
team of SiDock@home
|
|
| Results of the first iteration of the algorithm // Resultados de la primera iteración del algoritmo |
Dear volunteers,
We have good news! After processing the results of the first iteration, we have found a combination of model parameters that improves the behavior of the model compared to the initial one. In the original version, of the 100 markers that we are using, 77 were in the experimental range: now there are 80. On the other hand, the distance between the model and the average experimental behavior has been reduced by almost 30%.
The values of several of the parameters that have been modified are in the limit of the area that we had used in the first iteration, so the search area has been expanded (this is parameterized in the algorithm).
The tasks of the second iteration are already being sent. We will continue to inform you of how the results are going.
Thank you very much to all!
Best,
Jesús.
===============================================================
Estimados voluntarios:
¡Tenemos buenas noticias! Después de procesar los resultados de la primera iteración hemos encontrado una combinación de parámetros del modelo que mejora el comportamiento respecto del inicial que teníamos. En la versión original, de los 100 marcadores que estamos utilizando, 77 estaban en rango experimental: ahora ya están 80. Por otro lado, la distancia entre el modelo y el comportamiento medio experimental se ha reducido casi en un 30%.
Los valores de varios de los parámetros que se han modificado estan en el límite de la zona que habíamos utilizado en la primera iteracción, así que se ha ampliado la zona de búsqueda (esto está parametrizado en el algoritmos).
Ya están enviándose las tareas de la segunda iteracción. Os seguiremos informando de cómo van los resultados.
¡Muchas gracias a todos!
Un saludo,
Jesús.
|
|
| 12-digit factor of P2203 has now been found by the project... |
|
...398822 times
|
|
| Results of the last simulations and next steps // Resultados de las últimas simulaciones y siguientes pasos |
Dear volunteers,
I have both good and bad news to share with you regarding our recent progress. First, the good news: thanks to the results you've sent in, we have been able to identify the problem with the marker and gain a better understanding of what was happening. Additionally, it turns out that we won't need to increase the number of simulations per iteration, which is good news (for us).
However, there is also some bad news to report. We've discovered that the behavior of the model with this marker is highly non-linear, which means that it cannot be effectively addressed within the framework of our current approximation. While this could be disappointing, we can assume this limitation in the model, as it was measured experimentally under unrealistic conditions.
Once we've fine-tuned the model, we will determine whether this non-linear behavior persists, or whether it disappears with the changes we've made. If the issue does persist, we'll need to address it in the next phase of our work, which means there may be more work to come for some of you. We'll keep you updated on our progress.
We're grateful for your continued efforts and support.
Best regards,
Jesus.
===========================================
Estimados voluntarios:
Tengo noticias buenas y malas que compartir con vosotros sobre nuestro progreso reciente. Primero, las buenas noticias: gracias a los resultados que habéis enviado, hemos logrado identificar el problema con el marcador y obtener una mejor comprensión de lo que estaba sucediendo. Además, resulta que no necesitaremos aumentar el número de simulaciones por iteración, lo cual es una buena noticia (para nosotros).
Sin embargo, también hay malas noticias que reportar. Hemos descubierto que el comportamiento del modelo con este marcador es altamente no lineal, lo que significa que no puede ser abordado de manera efectiva dentro del marco de nuestra aproximación actual. Si bien esto puede ser decepcionante, podemos asumir esta limitación en el modelo, ya que se midió experimentalmente en condiciones poco realistas.
Una vez que hayamos ajustado el modelo, determinaremos si este comportamiento no lineal persiste o si desaparece con los cambios que hemos realizado. Si el problema persiste, tendremos que abordarlo en la siguiente fase de nuestro trabajo, lo que significa que puede haber más trabajo por hacer para algunos de ustedes. Os mantendremos informados sobre nuestro progreso
Muchas gracias por vuestro esfuerzo y apoyo continuo.
Atentamente,
Jesús.
|
|
| Aliquot sequence 60^53 has terminated!!! |
Aliquot sequence 60^53 has terminated!!!
|
|
| Citizen Science SETI Project at UCLA. |
Jean Luc Margot, a SETI Researcher at UCLA has started a Citizen Science project at UCLA. Participants will help identify and classify types of Radio Frequency Interference (RFI) seen in the data that they have taken at the Green Bank Telescope. This is an important step in identifying any signals that don't look like RFI.
You can join at https://www.zooniverse.org/projects/ucla-seti-group/are-we-alone-in-the-universe.
|
|
| Aliquot sequence 76^35 has terminated!!! |
Aliquot sequence 76^35 has terminated!!!
|
|
