HPC course – second edition – 24 September 2020

За втора година екипът на Лабораторията по високопроизводителни изчисления организира  обучение, свързано с използване на клъстер за високопроизводителни пресмятания (HPC).
Лектор ще бъде д-р Христо Илиев – експерт с голям опит в областта на Big Data и HPC (RWTH Aachen University, Germany 2011-2018;
2019-2020 Chief Data Scientist at holler.live, Amsterdam, Netherlands).

Планираме интензивно обучение за един работен ден -24 септември 2020 – ще има лекции, съпроводени с упражнения,
като ще ползваме MOODLE или друга електронна платформа.

Главни теми на обучението:

1. Отдалечен достъп до високопроизводителни изчислителни системи
2. Запознаване със системата за управление на разпределени ресурси (с други думи “с какво работата на споделен изчислителен клъстер се различава от работата на личното PC”)
3. Преглед на методите за програмиране на разпределени системи

Ниво на участниците – базови познания по Linux или друга Unix-подобна ОС (macOS, *BSD).

Добре би било да могат да редактират текстови файлове в конзолата с редактори като vim, Emacs, nano. Познания по програмиране на C или Python.

Моля,  разпространeте тази информация сред колегите, техните студенти, докторанти,
като заявки за включване в обучението да се изпращат до:

Стефка Близнева Stefka Blizneva <blizneva@fmi.uni-sofia.bg>

Ани Пройкова Ana Proykova <anap@phys.uni-sofia.bg>

Христо Илиев Hristo Iliev <hristo@hiliev.eu>

Срок за записване: до 17 септември 2020.        На записаните ще бъде изпратена подробна информация за начален час, платформа и изисквания.

С уважение,
проф. дфзн Ани Пройкова

Manifesto for EU COVID-19 Research

The Commission has launched a Manifesto today to maximise the accessibility of research results in the fight against Covid-19. The Manifesto provides guiding principles for beneficiaries of EU research grants for coronavirus prevention, testing, treatment and vaccination to ensure that their research results will be accessible for all and guarantee a return on public investment.

Manifesto for EU COVID-19 Research

 

New paper citing Nestum (link)

Capture and sequestration of greenhouse gases in Mn-based porous coordination polymers. https://doi.org/10.1002/chem.202001825
Capture and sequestration of greenhouse gases in Mn-based porous coordination polymers.
https://doi.org/10.1002/chem.202001825

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

Second Coronavirus Call for an Expression of Interest (European Commission)

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

European Commission – Green Deal Online Event

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.


Image is a link to the registration page

European Commission Online Learning Resources

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

Нашата работа по проекта Фолдинг – Covid 19/Doing our part of the Folding@Home project

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.

ChemRxiv COVID-19

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.