Nestum Cluster

A new publication in which the authors have cited Nestum has been published:

Effect of larger pore size on the sorption properties of isoreticular metal‐organic frameworks with high number of open metal sites
Pascal D. C. Dietzel, Peter A Georgiev, Morten Frøseth Rune E Johnsen, Helmer Fjellvåg, Richard Blom
First published:19 May 2020

The authors have kindly provided some amazing graphs and images for our gallery! You can review the publication at the following address: https://doi.org/10.1002/chem.202001825

Dear Researchers,
We would like to inform you that the second Coronavirus call for an Expression of Interest (H2020-SC1-PHE-CORONAVIRUS-2020-2) is now open on the Funding & Tenders Portal.

The links to the topics relevant to HPCL users are as follows:
1.SC1-PHE-CORONAVIRUS-2020-2B – Medical technologies, Digital tools and Artificial Intelligence (AI) analytics to improve surveillance and care at high Technology Readiness Levels (TRL)
2.SC1-PHE-CORONAVIRUS-2020-2D – Pan-European COVID-19 cohorts
3. SC1-PHE-CORONAVIRUS-2020-2E – Networking of existing EU and international cohorts of relevance to COVID-19

Please feel free to disseminate this information.
EUROPEAN COMMISSION, Research and Innovation

The EU’s goal of being carbon neutral by 2050 is under threat. The Covid-19 outbreak has forced EU member states to suspend business-as-usual and to focus on the immediate crisis, with the consequence that medium to longer term investment planning and goals relating to decarbonisation face an uncertain future. You can register for the free online event by clicking the image below.

Полезна информация при анализ на COVID-19

Useful information for COVID-19 analysis

http://link.tr.news-proteogenix.com/m/view/200118/500135/Yy79VOVBz7axaZoSutmbMg==?actId=ebwp0YMB8s0w7cV7ziTLodUcvuQDVN7agmFTt2FsrXtaLVHBd9s9CcBY_Ws8VVcC&actCampaignType=CAMPAIGN_MAIL&actSource=500135

From the European Commision website:

The outbreak of COVID-19 in Europe and necessary national measures taken to tackle the spread of the virus may cause significant disruption to the provision of education, training and mobility opportunities for learners, teachers and educators across the European Union (EU).

You can read, discover and use a variety of resources by following the link:

https://ec.europa.eu/education/resources-and-tools/coronavirus-online-learning-resources_en?fbclid=IwAR2vuLg_txB116C5fqktssesQsvPe_FOVKoa0hJjQVV_e52SAkw-FPs9Swo

Click here for English version

Благодарение на финансирането, осигурено от Министерството на образованието и науката
чрез Националната пътна карта за научно-изследователски инфраструктури,
Софийският Университет финансира оперативната дейност на Лабораторията по високопроизводителни изчисления (ЛВПИ)
по договор със Сдружението за научно-изследователска и развойна дейност, СНИРД.

Това финансиране осигури включването на ЛВПИ от 27.03.2020 г.
в международния проект Фолдинг – COVID 19, разработен в рамките на концепцията Отворена наука,
Екипът на ЛВПИ инсталира и изпълнява кода върху изчислителния клъстер Nestum http://hpc-lab.sofiatech.bg/

Целта на проекта, който включва световни екипи, е:
Да разберем как работят вирусните протеини (белтъци) и как можем да проектираме терапевтични средства, за да ги спрем.

Има много експериментални методи за определяне на структурите на протеините.
Макар и изключително мощни, те разкриват само единична снимка на обичайната форма на протеин.
Протеините обаче имат много движещи се части и за да видим протеина в действие е необходимо да симулираме всички възможни форми, които са стотици хиляди поради метастабилните състояния на неравновесните системи.
Системата атакуващ вирус-биологична клетка е неравновесна система. Структурите, които не можем да видим експериментално, може да са ключът към откриването на нов терапевтик.
Тези – невидени от експеримента структури – търсим да идентифицираме в компютърните симулации.

Повече за проекта може да намерите на уебстраницата https://foldingathome.org/covid19/.

С пожелания за добро здраве,
Екип ЛВПИ

In English

High performance computing laboratory (HPC) joins the project Folding at Home – COVID19

In light of the COVID-19 outbreak, the staff of HPC Lab has configured and is running a couple of jobs, part of
the Folding@Home project. Two of our compute nodes will be dedicated to this project for the time being.

You can learn more about the Folding@Home project by visiting their website at https://foldingathome.org/covid19/.

High performance computing laboratory (HPC) would like to acknowledge the Ministry of Science and Education for funding through the National Roadmap on Research Infrastructures
via Sofia University St. Kliment Ohridski that makes it possible to join the project Folding@Home – COVID19 .

Wishing good health,
HPC Team.

From: “ChemRxiv”
Date: 20 март 2020 21:51:39
Subject: Discover COVID-19 Research on ChemRxiv

In light of the current outbreak of a novel coronavirus (2019–nCoV), ChemRxiv would like to share this collection of preprints* on COVID-19. Chemistry has a key role to play in understanding everything from viral structure to pathogenesis, isolation of vaccines and therapies, as well as in the development of materials and techniques used by basic researchers, virologists, and clinicians.

ChemRxiv is openly accessible, with no subscription fees for readers and no submission charges for authors. We encourage you to read and share this collection with colleagues and also invite you to share your research with a global community of scientists by posting your COVID-19 research on ChemRxiv.

Read a Selection of COVID-19 Research:

A Single and Two-Stage, Closed-Tube, Molecular Test for the 2019 Novel Coronavirus (COVID-19) at Home, Clinic, and Points of Entry

Mohamed El-Tholoth, Haim H. Bau, and Jinzhao Song

Repurposing Therapeutics for COVID-19: Supercomputer-Based Docking to the SARS-CoV-2 Viral Spike Protein and Viral Spike Protein-Human ACE2 Interface

Micholas Smith and Jeremy C. Smith

Homology Models of the Papain-Like Protease PLpro from Coronavirus 2019-nCoV

Martin Stoermer

COVID-19 Disease: ORF8 and Surface Glycoprotein Inhibit Heme Metabolism by Binding to Porphyrin
Wenzhong Liu and Hualan Li

Computational Prediction of Mutational Effects on the SARS-CoV-2 Binding by Relative Free Energy Calculations
Junjie Zou, Jian Yin, Lei Fang, Mingjun Yang, Tianyuan Wang, Weikun Wu, Peiyu Zhang

Virtual Screening of an FDA Approved Drugs Database on Two COVID-19 Coronavirus Proteins

Alessandro Contini

Fast Identification of Possible Drug Treatment of Coronavirus Disease -19 (COVID-19) Through Computational Drug Repurposing Study
Junmei Wang

Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like Protease (3CLpro) Structure: Virtual Screening Reveals Velpatasvir, Ledipasvir, and Other Drug Repurposing Candidates
Yu Wai Chen, Chin-Pang Yiu, and Kwok-Yin Wong

Homology Models of Coronavirus 2019-nCoV 3CLpro Protease
Martin Stoermer

Molecular Docking Study of Novel COVID-19 Protease with Low Risk Terpenoides Compounds of Plants

Neda Shaghaghi

*Please note that ChemRxiv preprints have not been peer-reviewed and as such should be read with additional scrutiny. In the event that these preprints have subsequently appeared in a peer-reviewed journal, a link denoting this will appear on the page.

Dear users,

Due to the COVID-19 pandemic, the HPC Lab team will mostly refrain from spending time on-site as instructed by Sofia Tech Park. That being said, Nestum will continue to be available and online 24/7 and we will be accessible via email.

Ivo Iliev, a member of the HPC Lab team will attend this year’s instalment of The EuroHPC Summit Week (EHPCSW) 2020.

The conference will gather the main European HPC stakeholders from technology suppliers and HPC infrastructures to scientific and industrial HPC users in Europe. As in previous years, PRACE, the Partnership for Advanced Computing in Europe, organises the seventh edition of its Scientific and Industrial Conference (PRACEdays20) within the EHPCSW 2020. PRACEdays20 will bring together experts from academia and industry who will present their advancements in HPC-supported science and engineering.

For English, see below:

На 10.03 група от ученици от Софийска гимназия по строителство, архитектура и геодезия “Христо Ботев” ще посети Лаборатория по високопроизводителни изчисления. Проф. Пройкова ще изнесе доклад за използването на паралелни клъстери за практически цели.

On 10.03, a group of students from the SGCAG “Hristo Botev” will make a visit to the HPC laboratory. Prof. Proykova will give a lecture about practical applications of parallel clusters.