WCGrid News and Talking Points!!

[Arjai]

Help Cure Muscular Dystrophy Lead Researcher Releases Two New Open Data Tools


29 Jun 2017

Summary
In this letter to volunteers, Dr. Alessandra Carbone, the principal investigator for the Help Cure Muscular Dystrophy project, announces the release of two new open access tools which can accelerate the work of researchers who investigate protein interactions.

​

Dear volunteers for the Help Cure Muscular Dystrophy (Phase 2) project,

I am writing to update you on the analysis of the dataset of docking conformations produced by the Help Cure Muscular Dystrophy (HCMD2) project. The project’s goal was to investigate protein-protein interactions for more than 2,200 proteins whose structures are known, with a particular focus on those proteins that play a role in neuromuscular diseases.

The complete cross-docking dataset containing these protein-protein interactions is under analysis. For this, we are using the various computational tools that we developed in parallel with the calculations run on World Community Grid.

JET2 Viewer: A Repository of Protein Interfaces

We have built a database of protein interfaces for the scientific community. This database, called JET2, is a milestone for the identification of protein partners. Why is this important? The analysis of the HCMD1 and HCMD2 data highlights that a precise description of protein interfaces is crucial in discriminating protein partners, and the database produces a highly accurate set of such predictions. Improvement is still necessary, but the results are already very accurate.

We are now concentrating on extracting useful information relating to muscular dystrophy from the JET2 dataset that your support helped to construct. As you know, progress in research is slow, but we are making definite advances and expect that the methodological approach used in HCMD2 will be very successful in the large-scale identification of protein partners at protein-residue-level resolution! (A protein-residue is a portion of a protein.*)

BIS2Analyzer: A Server to Help Our Data Analysis

We have released a server, called BIS2Analyzer, to help identify signals of interaction based on coevolution analysis within proteins or between protein partners. This server, which is also openly accessible to the scientific community, is important because it can help to identify signals of protein interaction. It was useful to reconstruct the first protein-protein interaction network for viruses (see the reference below on the reconstruction of the network for the Hepatitis C Virus).

Thanking you again strongly for your contributions. I shall keep you updated on our results. Be assured that we are making progress, thanks to your support!

Best regards,

Alessandra

Best Regards to YOU, Alessandra!

 

[Arjai]

Potential New Treatments for Leishmaniasis Tested in Lab

By: Dr. Carlos Muskus López
Coordinator, Molecular Biology and Computational Unit, PECET University of Antioquia

1 Aug 2017

Summary
The Drug Search for Leishmaniasis team has begun lab testing potential treatments for this serious—yet neglected—tropical disease. In this update, Dr. Carlos Muskus discusses the results of topical (on the skin) testing of four compounds.

Background

Leishmaniasis is one of the most neglected tropical diseases in the world, infecting more than two million people in 98 countries. One form of the disease, caused by Leishmania infantum in America, mainly affects children, who can die if adequate treatment is not provided promptly. The classical treatments for all forms of Leishmaniasis can cause severe side effects, including death. Furthermore, drug resistant parasites are causing major problems in many endemic countries. For these reasons, there is an urgent need for new, safe, and inexpensive drug compounds.

Identifying Potential Compounds

After analyzing many compounds with the best docking score based on the data from the project on World Community Grid and our further testing, 10 compounds were finally selected to test in vitro. The in vitro evaluation involved cytotoxicity analysis against human-derived cell lines. (As part of the process of drug discovery, we do testing to ensure that the promising compounds do not affect human cells, thus decreasing the chance of side effects.) In addition, we evaluate the effectiveness of each compound against Leishmania, the parasites that cause leishmaniasis. The best compounds are those that kill the parasites at a low dose and do not affect the human cells even at higher doses.

Lab Testing of Potential Compounds

Next Steps

We still have a small remaining quantity of one of the compounds that produced some of the best result in the in vitro assay, but unfortunately the company that provided it did not synthesize it in sufficient quantity. We plan to contact another company to order more of this compound.

In addition, we are planning to re-test the compound that induced a complete cure in two of five hamsters. In future tests, we will probably change the method of administration to injection or oral, and closely monitor the outcomes.

Thank you to everyone who supported this project. We will keep you updated on our progress.

We also Thank You! For all your hard work in curing this disease!

More info/Technical stuffs about the Lab Testing is HERE

 

[Arjai]

Help Stop TB Uncovers New Data on Mycolic Acids

By: The Help Stop TB Team

University of Nottingham


17 Aug 2017

Summary
The Help Stop TB project is turning out to be the most comprehensive study of mycolic acids ever undertaken, which will be of enormous value to all researchers who are interested in how these molecules protect bacteria. In this update, the researchers describe mycolic acid folds that have never been detailed before, and explain how they plan to continue their exploration of this new territory as the project continues.

Hello everyone, and thank you for contributing your computer time to Help Stop TB!

Background

The bacterium that causes TB (mycobacterium tuberculosis) has an unusual coating which protects it from many drugs and the patient's immune system. This coating includes fatty molecules called mycolic acids. The Help Stop TB project is using computer simulations to simulate the behavior of these mycolic acids in their many configurations to better understand how they protect the TB bacteria. This may help scientists develop better treatments for this deadly disease.

Studying Mycolic Acids

Since our last update in February, the team has been focusing on analysing the simulation data that we’ve received from World Community Grid, and coming up with meaningful conclusions about how the different configurations of mycolic acids can offer protection to the TB bacteria. The mycolic acid folds that we will talk about in this section have not been described before, and there has never been such an in-depth study of mycolic acid folds and their relations to one another.

... utilizing a tool developed at the School of Pharmacy at the University of Nottingham, and distance matrix calculations. An example of the different information we can extract from distance matrix calculations can be found below.

This figure is an illustration of the distance matrix for two folds; a “knot” fold and a five-chain fold. These mycolic acid folds have not been described before. This figure shows that these different folds (left) are in fact connected and have dependencies with one another, as can be shown from their average distance matrices (right) that are quite similar visually. This similarity is further confirmed by root-mean-square deviation (RMSD) calculations.

These different folding patterns are currently in the process of being analyzed for the whole data set retrieved from World Community Grid.

The remaining challenge for the analysis of the World Community Grid data is to condense the vast amount of information into the important key features we are aiming for and the key question: why do distinct mycolic acids play such different biological and immunological roles? Stay tuned, we are working on it.

Future Plans

Future plans include letting our results “run dry” in a few months’ time. ... Additionally, new simulations will be added to the workflow based on the information we have already gathered.

In terms of team news, Athina is in her last weeks of thesis writing and needs to focus on that 100% to make sure submission goes smoothly! Once we “run dry” and start our simulations “clean”, our team will change slightly, as Wilma will be stepping down. Having initiated the project, Wilma has been pleased to see the project launch and make good progress with the hard work of the Nottingham team and your contributions. The entire team is extraordinarily grateful for Wilma’s contribution and talent—without her, we would never have embarked on this ambitious project, nor would we have had the insight to continue to expand it. She has contributed immeasurably and we wish her the best for her future endeavours—may they be at least as successful.

That was all our news for now! Thank you again for your contributions so far!

Edited slightly for size, the WHOLE thing is, HERE

"mycolic acids", eh? Could be the beginning of an end, to TB. This is Exciting, for me. As highlighted, we have, again, allowed researchers to discover something unknown. WORLD COMMUNITY GRID, the best thing I do, each day, by far. And by "do?" I leave my computer on and pay my electric bill. That's it! Changing the world has never been easier, or more fulfilling, than doing this. The discoveries by these teams, using the results we flood them with, is changing our world.

Thank You IBM and WCG!

 

[Arjai]

The Bacteria Inside Us: Gaining a New Understanding of Human Disease

By: The Microbiome Immunity Project research team



23 Aug 2017

Summary
What if you could help researchers learn more about how the bacteria in and on our bodies play a role in diseases such as Type 1 diabetes? We're proud to announce our latest project, which will be the first of its kind, large-scale, comprehensive study of the human microbiome.

What's the microbiome, and why is it important?

The human microbiome is a collection of all of the bacteria that live inside our bodies and all of the genes that they have. Scientists have found that we each have as many as 30 trillion bacteria in our own microbiome, and most of them live in our gut.

The bacteria in the microbiome are usually beneficial to humans. They can even be essential to our health. However, some are linked to diseases such as Type 1 diabetes, Crohn's disease, and ulcerative colitis. These diseases are becoming more common all over the world.

What's the microbiome's role in various diseases?

The short answer: scientists don't know exactly how the microbiome influences the beginning and development of disease, but they know that it plays an important role. That's why our group–consisting of researchers from the Broad Institute of MIT and Harvard, Massachusetts General Hospital, University of California San Diego, and the Simons Foundation's Flatiron Institute–is partnering with World Community Grid on the Microbiome Immunity Project. The project's goal is to study all the proteins (the building blocks of organisms) of the human microbiome, so that we and other researchers have a strong foundation to address these diseases.

In order to uncover the microbiome's role in the development of diseases, we need to first study the proteins produced by the bacteria in the microbiome. Learning about these proteins is important because proteins perform cell functions– they can interact with each other to form larger structures, they can carry out chemical reactions, bind on to other macromolecules in the cell, transport smaller molecules, or carry out a host of other roles within cells.

So far, there has not been a study of the human microbiome on this scale. Researchers have studied individual bacteria and specific proteins in the microbiome, but never all the proteins that are made by all the different bacteria. When you have trillions of bacteria to study in the gut alone, this becomes a monumental task.

We, like most research organizations, don't have anywhere near the amount of computing power needed to take on such a task.

You can help!

We're enlisting the help of volunteers like you from all over the world to support the Microbiome Immunity Project. Together, World Community Grid volunteers provide researchers like us with the enormous computing power we need to carry out studies that would not otherwise be possible.

Here's how it works: ....
To contribute to the Microbiome Immunity Project, join World Community Grid, or if you are already a volunteer, make sure the project is selected on your My Projects page.

Fresh Project!! Get 'em while they're HOT!!

I have one, on each machine, so far. The earliest one I have is from Tuesday morning. They look to be small in size, so far. Could be good, if they stay that way, been looking to add another easy one for my Android phone to crunch!

So, yea. Here it is, the NEW Project!! Let's bury 'em with results!! Ready, Set, GO!!!

 

[Arjai]

Well, um, after doing a slight bit of research on this NEW Project. No Android.

I guess I cannot expect everything from the NEW guys! It's OK.


Oh, HERE, are the requirements, for this and all the projects...

 

[Arjai]

NEW BOINC!!

http://boinc.berkeley.edu/download.php

7.8.2
No notes on it, that I could find. But, I am going for it now. I will update tomorrow, how it goes. Then maybe Tuesday, switch the Linux boxes over.​

 

[Arjai]

Plans for Future Development Discussed at BOINC Workshop 2017

22 Sep 2017

Summary
A group of BOINC developers, project managers, researchers, and volunteers recently participated in a workshop where they exchanged information and ideas that will help set the direction for the future development of the BOINC open source project.

The BOINC Workshop 2017 was held in Paris on September 6-8. This was the first such gathering since BOINC (the software on which World Community Grid and other distributed computing projects are built) transitioned to a community governance model in 2015. World Community Grid technical team members Kevin Reed and Keith Uplinger represented World Community Grid at the event.

​

Does anyone else feel that Mr. Reed looks a little ghostly?

​

The workshop's primary purposes were to connect members of the BOINC community, share information about the various projects that use BOINC, and discuss future plans for the continued development of the platform. Some of the items discussed were:

• Demonstration of a proof-of-concept that enables communication between a user's browser and the BOINC client, which could potentially be used to simplify how volunteers register and attach to World Community Grid
• The progress of a new National Science Foundation grant to enable the use of BOINC with resources such as Purdue University's nanoHUB
• Rapidly setting up a BOINC project using docker (a system that lets developers create apps in the environment of their choice)
• Running a research application within a docker container
• Automated testing of BOINC server code, which will help improve code quality

World Community Grid's Keith Uplinger gave the group an update about how World Community Grid uses DevOps (a software development method that helps communication and collaboration between software developers and IT personnel). Kevin Reed, who serves as Chair of the BOINC Working Committee, gave a report on the committee's current tasks and goals, which include increasing the number of volunteer developers who contribute regularly to the development of BOINC.

Other presentations included an update on BOINC project climateprediction.net, which is the world's largest climate modelling experiment; and a talk about the BOINC Pentathlon, a 14-day online event which brings in new volunteers from all over the world.

For more information about the BOINC Workshop 2017, visit the event website.

From the event website...

​

Participant List

35 participants
Andrey Voronkov Digital BioPharm ltd.
Andy Bowery Oxford University
Bernd Machenschalk Albert-Einstein-Institute
Bruce Allen Albert Einstein Institut Hannover
Carl Christensen
Christian Beer Einstein@Home (Albert-Einstein-Institute)
Christian Köckritz
David Anderson UC Berkeley
David O'Connor Team Gridcoin
David Wallom Unviersity of Oxford
Eamonn O'Connor Team Gridcoin
fayssal sarghini
Frederick McIntosh CERN
George Emsden BOINC volunteer since 1999 and OU Science student
Ivan Reid Brunel University London (GB)
Joachim Becker-Bergemann User / Foerderverein der Carl-Schurz-Schule in Frankfurt am Main
Joël Duet Gridcoin community
Keith Uplinger World Community Grid
Kevin Reed IBM/World Community Grid
Krzysztof Piszczek DrugDiscovery@Home, Universe@Home
Laurence Field CERN
Laurent Domisse IAP
Marius Millea Institut Lagrange de Paris
Matt Blumberg GridRepublic + Charity Engine
moussaoui moussa
Nils Hoimyr CERN
Oliver Bock Einstein@Home
Olivier Fehr Olivier Fehr Media
Patrick Schoefer SETI.Germany
Richard Csabai
Richard Haselgrove
Richard Main
Romain Pouzol
Steven Clark Purdue University
Valera Rozuvan

​

2 things, I hadn't heard about this and I want to go to Paris. TPU should have sent me, the WCG reporter,to Paris to cover this!

 

[Arjai]

No worries, those were corrupted links that I effed up and then figured out. Why they are un-edit-able, IDK. But, you have all the content, Plus a few corrupted, x-ed out mistakes.

 

[Arjai]

The Road Ahead for Help Fight Childhood Cancer

By: Dr. Akira Nakagawara, MD, PhD CEO of the Saga Medical Center KOSEIKAN and President Emeritus, Chiba Cancer Center

26 Sep 2017

Summary
The Help Fight Childhood Cancer researchers discuss how they’re moving forward with data analysis and continuing their search for pharmaceutical partners.

​

Background

The Help Fight Childhood Cancer (HFCC) project was created to look for better treatments for neuroblastoma, which is refractory among childhood cancers (meaning that it is resistant to treatment). The project’s goal was to target certain cell proteins regulating cancer cell growth—such as TrkB tyrosine kinase receptor, ALK tyrosine kinase receptor, N - CYM protein and others—with the help of World Community Grid’s enormous computing power, which is donated by an international community of volunteers.

Looks as though they found something interesting...

Our research team conducted in-silico (computer simulation-based) drug discovery screening using World Community Grid to search through a library of three million small molecular compounds. We discovered a small molecule compound which competitively binds to the TrkB protein pocket to which BDNF (a specific growth factor) binds. The discovered molecule can thus prevent BDNF from binding to the TrkB protein and diminish cancer cell growth. This could lead to a new and improved treatment for neuroblastoma.

Subsequently, the anti-tumor effect of the compound was examined using cultured cancer cells, or human neuroblastoma transplanted into mice, and this laboratory research confirmed that this small molecular compound and possibly some others could be candidates for anticancer drugs targeting TrkB. We announced this breakthrough and published our findings in the peer-reviewed, English language journal, Cancer Medicine, in 2014.

Current Research

Currently, we are conducting research to develop even more potent inhibitors by synthesizing small molecular compounds similar in structure to the compounds found using the screening. The road to developing commercial, approved new drugs is a tough task. We must find a pharmaceutical company that will conduct joint research and development and create a patentable compound so that this expensive effort is profitable. If any of you have contacts with a pharmaceutical company that may be interested in pursuing this venture, please introduce us.

Anybody got contacts to the big Pharm's?

Additionally, using World Community Grid to screen drug candidates, we found other small molecular compounds showing the ability to inhibit the ligand BDNF. These results were presented it in another English language journal (Neurochem International, 2016, abstract here). These compounds also look promising as a remedy for depression and dementia, and similarly, we are seeking a pharmaceutical company to cooperate in research and development of these.

Yet again, something I love, a focused project we flood with data, finds answers to things they weren't looking for!

The N-CYM is a new protein we discovered which is implicated in neuroblastoma. A published paper about this can be found here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3879166/. Before we can screen for drug candidates, we must determine this protein's three-dimensional structure. Therefore, we are currently working on the difficult task of crystallizing the N-CYM protein so that we can perform X-ray analysis to determine the protein’s three-dimensional structure. Once the three-dimensional structure of the protein is determined, we will screen to find inhibiting compounds in the Smash Childhood Cancer project, which is building on the work from this project.

"We thank all volunteers who supported this project, and look forward to keeping you updated on the progress of this project as well as the Smash Childhood Cancer project."

More here, enjoy!

 

[Arjai]

A Volunteer in France on Why He Joined World Community Grid

By: Gil Rivet Crunchers Sans Frontieres

29 Sep 2017


Summary
Meet Gil Rivet, a volunteer from France who is an administrator for the Crunchers Sans Frontieres team. Here's his story in his own words.

​

....

My participation in the World Community Grid project can be summarized as follows: Use my computer to process data, which cannot be done by my brain. As long as World Community Grid has humanitarian projects, I will continue to be motivated to participate.

Not quite sure how this became a post on WCG. But, it is.

For more of this AMAZING STORY confused, Click HERE

 

[Arjai]

Open Zika Researchers Continue Calculations, Share the Wealth, and Spread the Word

By: The OpenZika research team

3 Oct 2017

Summary
The OpenZika researchers are continuing to screen millions of chemical compounds as they look for potential treatments for the Zika virus. In this update, they report on the second stage of the project, using a newly prepared, massive library of 30.2 million compounds that are being screened against the Zika virus proteins. They also continue to spread the word about the project.

Project Background

The Zika virus has “evolved” from a global health emergency to a long-term threat. Scientists throughout the world continue to study the virus and search for ways to stem its spread, including potential vaccines and means of controlling the mosquito population, as well as looking for treatments. As of this update, there is still no vaccine for the Zika virus, and no cure.

We remain convinced that the search for effective treatments is crucial to stemming the tide of the virus. In addition to the OpenZika project, several other labs are doing cell-based screens with drugs already approved by the U.S. Food and Drug Administration (FDA). Still, few to none of the compounds that have been identified thus far are both potent enough against Zika virus and also safe for pregnant women.

Continuing progress on choosing compounds for lab testing

We are continuing the analysis phase of the project, focusing on the results against the new target structures solved for NS3 helicase, NS5 polymerase, NS2B-NS3 protease, and NS1 glycoprotein.

To select the NS3 helicase candidates, we have been using distinct approaches for filtering and analyzing the virtual screening results. The first one is target specific, based on molecular docking calculations. Since there are two crystal derived structures of helicase (with and without RNA-bound) in the PDB (Protein Data Bank, a database that stores and freely distributes atomic-resolution structures of biological macromolecules), we docked approximately 7,600 compounds in a composite library composed of the U.S. Food and Drug Administration-approved drugs, the drugs approved in the European Union, and the U.S. National Institutes of Health clinical collection against both of these structures of NS3 helicase. The docking results were then filtered by the estimated binding free energy (the docking score) and by the minimum number of hydrogen bonds that were predicted to form with the helicase target, followed by visual inspection of the predicted binding modes.

Subsequently, in a second workflow the candidates passed through developed and validated QSAR models (Quantitative Structure-Activity Relationship), which are based on phenotypic data (cell-based assay results) on the Zika virus available in the PubChem Bioassay Database (AID1224857).

After visually inspecting the structures of the compounds to detect medicinal chemistry related liabilities, we selected 9 candidates and ordered them. They are currently being assayed by our collaborator at the University of California, San Diego, in Dr. Jair L. Siqueira-Neto’s lab.

• Workflow 1: 232 compounds passed a collection of different energetic and interaction-based docking filters, and their predicted binding modes were visually inspected by Dr. Alexander L. Perryman, to select the candidate compounds that were discussed in our previous project update. These candidates are currently being assayed by Professor Shan-Lu Liu’s lab at The Ohio State University.
• Workflow 2: These 232 compounds were then scored with the consensus QSAR model (trained with cell-based Zika assay data), and 74 compounds passed this additional filter. The docked binding modes of these 74 compounds were inspected in detail by Dr. Melina Mottin and Dr. Carolina Horta Andrade.
• Of the compounds that passed the inspection of their docked modes, 9 passed subsequent medicinal chemistry-based inspection (by Dr. Sean Ekins and Professor Joel Freundlich), were ordered, and are currently being assayed by Dr. Siqueira-Neto.

Status of the calculations

...
Thus far, the > 80,000 volunteers who have donated their spare computing power to OpenZika have given us > 34,000 CPU years worth of docking calculations, at a current average of 73 CPU years per day! Thank you all very much for your help!!

A new stage of the project, and sharing the wealth

As described above, instead of docking 6 million compounds, we are now screening a new library of 30.2 million compounds against all the ZIKV targets. This new, massive library was originally obtained in a different type of format from the ZINC15 server. It represents almost all of “commercially available chemical space” (that is, almost all of the “small molecule” drug-like and hit-like compounds that can be purchased from reputable chemical vendors).

The ZINC15 server provided these files as “multi-molecule mol2” files (that is, up to 100,000 different compounds were contained in each “mol2” formatted file). These files had to be re-formatted (we used the Raccoon program from Dr. Stefano Forli, who is part of the FightAIDS@Home team) by splitting them into individual mol2 files (1 compound per file) and then converting them into the “pdbqt” docking input format.

By splitting, reformatting, and testing hundreds of thousands of compounds per day, day after day, after approximately 6 months this massive new library of compounds was prepared and ready to be used in our OpenZika calculations. Without the tremendous resources that World Community Grid volunteers provide for this project, we would not even dream of trying to dock over 30 million compounds against many different targets from the Zika virus. Thank you all very much!!!

Soon after we started using this new massive library for our virtual screens in OpenZika, Viktors Berstis at IBM/World Community Grid put us in contact with Dr. Akira Nakagawara, the principal investigator of the Smash Childhood Cancer project. To help expand the scope of their experiments that search for new cancer drugs, we gave them a copy of our new library of 30.2 million compounds.

For more information about these experiments, please visit our website.

Publications and Collaborations

OpenZika project results were presented on July 7-14 at an International Conference, the 46th World Chemistry Congress, in Sao Paulo, Brazil, which had almost 3,000 attendees.

The slides from her presentation are available on SlideShare.
​

We will be presenting a poster at Cell Symposia: Emerging and Re-emerging Viruses, on October 1-3, 2017, in Arlington, VA, U.S.A:

Title:

OpenZika: Opening up the discovery of new antiviral candidates against zika virus

Authors:

A.L. Perryman, M. Mottin, R.C. Braga, R.A. Da Silva, S. Ekins, C.H. Andrade

Presenting Author:

S. Ekins

We have also recently published another research paper entitled “Molecular Dynamics simulations of Zika Virus NS3 helicase: Insights into RNA binding site activity” in a special issue on Flaviviruses for the journal Biochemical and Biophysical Research Communications. This study of the NS3 helicase system helped us learn more about this promising target for blocking Zika replication. The results will help guide how we analyze the virtual screens that we performed against NS3 helicase, and the Molecular Dynamics simulations generated new conformations of this system that we will use as targets in new virtual screens that we perform as part of OpenZika.

Additional News

Dr. Sean Ekins has hired a postdoctoral scientist and a master’s level scientist who will get involved with the OpenZika project. We have also started to collate literature inhibitors from Zika papers.

Also, Drs. Sean Ekins and Carolina Andrade have bought some of the candidate compounds that we identified in the virtual screens from OpenZika, so that they can be assayed in the next round of tests.

Fundraising

​

Thank you to anyone who has visited our store on Zazzle to check out OpenZika merchandise, such as T-shirts, polo shirts, mugs, buttons, mouse pads, tote bags, hats, ties, pillows, key rings, and phone cases that have the OpenZika logo! All profits that we receive from the sale of this merchandise will go toward buying compounds for lab testing.

The OpenZika team is working on grants from the National Institutes of Health (NIH), CNPq and FAPESP (Brazilian funding agencies), and other organizations to try raise funds for purchasing and testing compounds. In May 2017, Rutgers University gave Dr. Perryman “Principal Investigator” status for NIH grant purposes. Consequently, in June he submitted his first grant application, which focuses on the OpenZika results against the NS2B-NS3 protease. In August, Dr. Perryman and Dr. Ekins submitted an NIH grant together, which also focuses on the results of docking 30 million compounds against the NS2B-NS3 protease.

Outreach

We have been working hard to promote the project, and we continue to look for additional opportunities. Below is a list of our most recent outreach efforts.

• Dr. Carolina Horta Andrade gave one invited lecture at the State University of Sao Paulo (UNESP), in Sao Jose do Rio Preto – SP, to biology, chemistry and pharmacy students regarding the “Computational approaches for the design and discovery of new drug candidates for the Zika virus” (April 20, 2017)
• Dr. Carolina Horta Andrade participated in the Pint of Science Brazil (May 15-17, 2017) and presented a lecture regarding drug discovery for tuberculosis to Zika, in a beer bar full of young people.

• Dr. Carolina Horta Andrade gave an invited lecture at the National Health Conference – CONMSAÚDE regarding drug design and discovery for Neglected Tropical Diseases (May 26, 2017).
• Dr. Melina Mottin, one of the OpenZika team members, gave an invited oral presentation, titled “OpenZika: Opening the discovery of new antiviral candidates against Zika virus and insights into dynamic behavior of NS3 Helicase,” at the 46th World Chemistry Congress, in Sao Paulo, Brazil, on July 7-14.
• Dr. Carolina Horta Andrade gave an invited lecture at the Brazilian Young Medicinal Chemistry Scientists Workshop, at the University of Sao Paulo, Brazil, regarding “Experimental and computational approaches integrated for the discovery of new drug candidates,” for the general public, as well as to pharmacy and chemistry students (June 12, 2017).
• OpenZika project update has been released on some Brazilian news channels and websites:
  • https://www.ufg.br/n/96147-ufg-descobre-novos-possiveis-compostos-contra-o-virus-zika
  • http://diaonline.com.br/video-on-demand/projeto-open-zika-da-ufg-para-a-vacina-contra-o-virus-zika/
  • http://g1.globo.com/goias/noticia/u...-podem-ajudar-a-tratar-pessoas-com-zika.ghtml

We are very grateful for all the volunteers who are donating their unused computing time to this project! Thank you very much!!

WOW! Lot's of progress and a big News Report!!
For all of it, Click HERE

Keep up the Good Work, and buy something from their store!!

 

[Arjai]

https://www.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=540
Thursday maintaince, they say an hour. We hope they are correct.

 

[Arjai]

Discovering Dengue Drugs - Together Takes a New Approach to Data Analysis

By: Dr. Stan Watowich, PhD

University of Texas Medical Branch (UTMB) in Galveston, Texas



18 Oct 2017

Summary
In this update, Dr. Stan Watowich, principal investigator for the Discovering Dengue Drugs - Together project, explains how the research team is shifting their approach to data analysis. The research team has also released their best-scoring results in order to help other scientists conducting similar studies.

We wish to thank the World Community Grid volunteers for their support over these past years.

The World Community Grid phase of our "Discovering Dengue Drugs – Together project completed its computations a while ago. The mission of the project is to identify promising drug candidates to combat dengue, hepatitis C, West Nile, yellow fever, and other related viruses.

As noted in a previous update, we have been analyzing the results, retesting some of the calculations, modifying the underlying assumptions for the calculations, and testing compounds in the laboratory using in vitro (test tube/culture dish) and in vivo (in living organisms) systems. We have worked with our medicinal chemists to synthesize variants of several initial inhibitor "hits" with the goal of improving their activity for planned pre-clinical trials. Our current designs, unfortunately, have not yet produced a highly potent dengue protease inhibitor suitable for in vivo testing. Thus, we are shifting our approach for this project and are now screening combinatorial chemistry libraries for protease inhibitor "hits" to use as starting points for "hit-to-lead" improvement. Free energy perturbation calculations and 3-D structure-guided design will be used to improve the potency and physiochemical properties of these hits.

The links below contain the ~1000 lowest (best) scoring small molecules predicted to bind to the catalytic site of NS2B-NS3 proteases from dengue and West Nile viruses that were used in this virtual screening project. We hope this information may be of use to other investigators in their development of computational chemistry tools and/or dengue antivirals.

Dengue virus protease (PDB 2FOM)

West Nile virus protease (PDB 2FP7)

West Nile virus protease (PDB 2IJO)

Let's hope the new testing works!

 

[Arjai]

Planned Maintenance on Wednesday, October 25

That is today. Right Now! I only noticed due to a WU sitting and waiting to upload.

More HERE.

 

[Arjai]

Release Notes for BOINC 7.8

New BOINC out there!

Changes in 7.8.3

• 
  
  
  • client: extensions, fixes to account manager functionality
  • client: eliminate possible buffer overflow in reporting result errors
  • lib: fix boinc_file_exists() on Windows
  • Mac: Changes to Xcode project to support screensaver changes for Mac OS 10.13.
  • Screensaver: Changes for screensaver to support Mac OS 10.13
  • api: BOINC graphics library changes to support Mac OS 10.13
  • client library: inconsistent terminology for intel_gpu
  • update project list
  • Locale: Update french localization files
  • update installshield files

• 
  

I am SOOOO glad they fixed those French localization files!! Man has that been a pain!

Get it!! Get it HERE!

 

[Arjai]

The Whats and Whys of Basic Research

31 Oct 2017

Summary
What is basic research and how is it applicable to the work done on World Community Grid? In this article, we'll address some of the fundamental questions about basic research, which is the foundation of scientific discovery.

“Basic research is performed without thought of practical ends. It results in general knowledge and understanding of nature and its laws. The general knowledge provides the means of answering a large number of important practical problems, though it may not give a complete specific answer to any one of them.”

Vannevar Bush,
"Science, the Endless Frontier"

What is basic research?

When scientists study a phenomenon, a particular subject, or a natural law, with the primary intention of understanding what they’re studying, they’re conducting basic research. This type of research, which can be conducted in any branch of science, is meant to add to and strengthen the very core of scientific knowledge.

On the other hand, applied research, which involves testing possible applications of theories and methods, often gets more attention than basic research because it can more directly result in new discoveries. But applied research depends on the accumulation of knowledge that is only possible from many basic research studies, some of which are branded as “failures” before they turn out to have applications that the original researchers never may have guessed.

In the scientific world, there’s often not a clear division between basic and applied research. Many World Community Grid projects could be considered a combination of both. For example, the Mapping Cancer Markers project, which is looking for biomarkers for various types of cancer, can be considered basic research in that it involves sifting through massive amounts of raw data in a new way, but is also applied research because its goals—such as helping find personalized treatments for cancer—are concrete.

The researchers for the Computing for Clean Water project (described in the video above) discovered a phenomenon that could improve water filtration technology and desalination.
​

Why is it crucial for continued scientific discovery?

Future discoveries depend on the basic research of yesterday and today. And basic research projects often uncover knowledge no one expected, and lead to paths that were previously unknown.

One recent example for World Community Grid researchers occurred in 2016, when the Help Fight Childhood Cancer researchers discovered that two of the chemical compounds they were studying for their effectiveness against neuroblastoma might be useful in developing a treatment for depression and dementia.

Why is public involvement in this type of research so important?

“Basic research is often misunderstood, because it often seems to have no immediate payoff.”

Massachusetts Institute of Technology,
"The Future Postponed"

Public funding for all types of science has been declining in many countries for a number of years. For example, researchers in Argentina and Brazil have experienced steep decreases in federal funds, and in 2016 scientists in Italy launched an online petition for greater funding that received more than 77,000 signatures. When scientific funding is cut, the sparse remaining monies are often allocated to projects that are viewed as having a quicker “payoff,” such as the proposed 2018 budget for the USA’s National Science Foundation that cuts funding to certain graduate fellowships while prioritizing other programs.

“Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world.”


Louis Pasteur

More of this Story, HERE

Interesting quotes from the Science World and some definitions of terms, some non-scientist's may find enlightening.

 

[Arjai]

Analysis Underway on 30 Terabytes of Data from the Uncovering Genome Mysteries Project

24 Nov 2017

Summary
The Uncovering Genome Mysteries data (all 30 terabytes) was transferred to the research teams in Brazil and Australia this year. Now, the researchers are analyzing this vast amount of data, and looking for ways to make it easy for other scientists and the public to understand.

In this video, Dr. Torsten Thomas explains the primary goals of the Uncovering Genome Mysteries project.
I found this video to be a little hard to understand, first time through. The sound has a bit of contrast, making it hard to hear. I closed my eyes and listened to it a couple of times before I could make it out.​

Background

Last year, World Community Grid volunteers completed the calculations for the Uncovering Genome Mysteries project, which examined approximately 200 million genes from a wide variety of life forms to help discover new protein functions. The project’s main goals include:

• Discovering new protein functions and augmenting knowledge about biochemical processes in general
• Identifying how organisms interact with each other and the environment
• Documenting the current baseline microbial diversity, allowing a better understanding of how microorganisms change under environmental stresses, such as climate change
• Understanding and modeling complex microbial systems

Transferring 30 Terabytes of Data

The data generated by World Community Grid volunteers has been regrouped on the new bioinformatics server at the Oswaldo Cruz Foundation (Fiocruz), under the direction of Dr. Wim Degrave. Additionally, a full copy of all data has been sent to co-investigator Dr. Torsten Thomas and his team from the Centre for Marine Bio-Innovation & the School of Biological, Earth and Environmental Sciences at the University of New South Wales in Sydney, Australia. At the University of New South Wales, the results from protein comparisons will help to interpret the analyses of marine bacterial ecosystems, where micro-organisms, coral reef, sponges and many other intriguing creatures interact and form their life communities. The dataset, more than 30 terabytes under highly compressed form, took a few months to be transferred from Brazil to Australia.

Data Processing and Analysis at Fiocruz

Some of the data are currently being used in projects such as vaccine and drug design against arboviruses such as Zika, dengue, and yellow fever viruses, but also for understanding of the interaction of bacteria with their environment and how this reflects in their metabolic pathways, when free living bacteria are compared with their close relatives that are human pathogens, such as Mycobacterium tuberculosis versus environmental mycobacteria.

Searching for Partnerships

Fiocruz is looking for partnerships that would add extra data analytics and artificial intelligence to the project. The researchers would like to include visualizations of functional connections between organisms as well as particularities from a wide variety of organisms, including deep sea thermal vent archaeal bacteria; bacteria and protists (any one-celled organism that is not an animal, plant or fungus) from soil, water, land, and sea or important for human, animal, or plant health; and highly complex plant, animal, and human genomes.

We thank everyone who participated in the World Community Grid portion of this project, and look forward to sharing more updates as we continue to analyze the data.

Some info was not copied to this post. For the Whole article, Click HERE.

 

[Arjai]

New Facility and Expanded Plans for the Mapping Cancer Markers Research Team

By: Dr. Igor Jurisica
Krembil Research Institute, University Health Network, Toronto

30 Nov 2017

Summary
The Mapping Cancer Markers researchers recently moved to a new institute, but continues analyzing results, planning for expanded research, and creating new work units throughout the transition. Learn about their plans in this article.

Background

The Mapping Cancer Markers (MCM) project continues to process data to identify biomarkers for ovarian cancer. We are also in the process of analyzing MCM results from the lung cancer dataset, and we are finalizing preparation of the new work units for sarcoma, a type of malignant tumor. We will devote more space in the next project update to this work. Below we provide details about an exciting new development in the team.

The Move

After more than 17 years at Ontario Cancer Institute (now Princess Margaret Cancer Centre), we got an opportunity to join Krembil Research Institute (KRI) to work on a more complex approach to chronic diseases, where we moved in mid-November. ..the physical move was smooth, and our severs stayed in the original server rooms, reducing the risk of any hiccup for World Community Grid work units and results. We will not only continue, but will expand on our research..

New Computational Biology Platform

Importantly, we are in the finalizing stages of paperwork to embark on a newly-funded research by the Ontario Government: The Next Generation Signalling Biology Platform. This will provide us funds to create a software infrastructure for the comprehensive, integrative computational biology analyses workflows, in collaboration with translational research and clinical trials groups.

Thank you to everyone for your support, and we look forward to providing additional updates as our work progresses.

Edited for size, the Whole Story, HERE.

 

[Arjai]

Planned Maintenance on Saturday, December 9 (Completed)

Summary
We are upgrading the software on multiple parts of the system on Saturday, December 9, beginning at 2:00 UTC.

Update: This work has been completed. It finished at 3:55 UTC. Thanks for participating!

Um, it is Friday and their done already?

 

[Arjai]

Sustainable Water Data Available to Interested Scientists

By: Gerard P. Learmonth Sr., M.B.A., M.S., Ph.D.
University of Virginia

14 Dec 2017

Summary
Dr. Gerry Learmonth, the principal investigator for the Computing for Sustainable Water project, gives an update on the primary findings of the project as well as how other scientists can access the data.

​

Project Background
The Computing for Sustainable Water project was created to study the effects of potential management practices on the Chesapeake Bay Watershed, a large watershed in the southeastern United States, and to gain deeper insights into what actions can lead to restoration, health, and sustainability of watersheds around the world.

Our Results
The project is now finished. For all the contributors on the World Community Grid – a sincere thank you! The project started when then President Obama issued an Executive Order to restore and sustain the quality of the Chesapeake Bay Watershed. This project involved a very detailed simulation of the Bay with the goal of better understanding the impact of a set of practices—in fact, best management practices—on achieving that goal.

Further Reading and Data
Please check out the Computing for Sustainable Water website. There you will find a new, as yet unpublished paper about the project, entitled “Impact of Best Management Practices on Water Quality.”
For other scientists and others interested in doing a deep dive into the data, we’ve also created a document describing how the results of the experiments are formatted, and how to request data from particular experiments. We invite anyone doing research in this area to make use of the data.

"To all the World Community Grid volunteers who donated to this project – thank you!"

More of the Story, HERE.

 

[Arjai]

Planned Maintenance on Saturday, January 6

4 Jan 2018

Summary
We are updating the operating system on our servers on Saturday, January 6, beginning at 2:00 UTC.

We will be applying an important operating system update to our servers on Saturday, January 6, beginning at 2:00 UTC. We anticipate that the work will take approximately four hours.
During this time, volunteers will not be able to upload or download new work. The website will not be accessible during this time. No action is required by volunteers, as devices will automatically retry their connections after the maintenance work is completed.

We appreciate your patience and participation.

Plan accordingly!

 

[Arjai]

Computing for Clean Water Results Inspire Further Study

By: The Computing for Clean Water team
22 Jan 2018

Summary
An international team of researchers was inspired by the Computing for Clean Water project to do a series of further simulations, using a slightly different model and studying the diffusion of oxygen molecules as well as water molecules. Learn about their results, which validated the work done on World Community Grid, in this article.

Background
The Computing for Clean Water project was created to provide deeper insight on the molecular scale flow of water through a novel class of filter materials. Thanks to the millions of virtual experiments that the team was able to run on World Community Grid, they discovered conditions under which water can pass through tiny carbon nanotubes much more efficiently. This groundbreaking understanding of a fundamental physical process could help improve access to clean water for millions of people through more efficient water filtration and desalination, and also may have applications in clean energy and medicine.

The Value of Independent Verification
...
The story behind these articles illustrates an important point in science: the value of independently verifying new results. In this case, an international team with lead author Eduardo Cruz-Chú at ETH Zurich was inspired by our results to do a series of complementary simulations. The team used a somewhat different model of the water flow, and also focused on the diffusion of oxygen atoms in the water.
...
These authors did, however, obtain a smaller diffusion enhancement using their model than what we had reported in our study. In the field of molecular dynamics simulations, it is quite common to see some variations depending on the details of the models used. So, we did a series of further simulations to test the robustness of our original results. What we found is that the effect of phonons on the water diffusion is always large compared with a phonon-free calculation, even allowing for considerable variation in some of the parameters used in our model.

Differences between Studies
A significant difference between the two studies concerns the type of diffusion that is being monitored – we only considered water molecules, whereas our colleagues studied also the diffusion of oxygen atoms. Their results suggest that the diffusion of other molecules or ions will be different. This difference is something that we hope to study in future, since it has implications for how effective nanotubes can be in filtering out unwanted molecules and ions, for example salt ions from seawater.
...
In the end, the ultimate arbiter of the importance of simulated results like ours will be hard experimental data. You can read our detailed response to the new article here.

In the meantime, we thank all World Community Grid participants in Computing for Clean Water for helping to obtain the original results, which are clearly getting the attention of the scientific community.

Excellent news. More stuffs than planned, from the initial work, is always good news!

Read the entire post, this has been edited, click this link to the WCG Page.

 

[Arjai]

Hmmm, it has gotten a little quiet in here. Are my posts getting too boring? Do I need to change the format? I know that the text palette has changed and the colors are more muted...

Is this Color even readable?
Is this Color even readable?
Is this Color even readable?
Is this Color even readable?
Is this Color even readable?
Is this Color even readable?
Is this Color even readable?
Is this Color even readable?
Is this Color even readable?
Is this Color even readable?
Is this Color even readable?
Is this Color even readable?
None of these colors have any POP
The blue, from the last palette, was a bit bolder.

Case in Point... Old Blue
and the New Blue

Old Blue

New Blue

Another New Blue

No POP!!

It's like sleepy time around here!

I WANT MY BLUE BACK!!!!!​

@W1zzard ?

 

[Arjai]

Planned Maintenance on Monday, February 12

8 Feb 2018

Summary

We are updating the operating system on our servers on Monday, February 12 beginning at 15:00 UTC.

We will be applying an important operating system update to our servers on Monday, February 12, beginning at 15:00 UTC. We anticipate that the work will take approximately four hours.

During this time, volunteers will not be able to upload or download new work, and the website will not be accessible. No action is required by you, as your devices will automatically retry their connections after the maintenance work is completed.
We appreciate your patience and participation.

Hope it goes smoothly!

 

[Arjai]

Planned Maintenance on Monday, March 5

1 Mar 2018

Summary
We are performing database updates on our servers on Monday, March 5 beginning at 18:00 UTC.

We will be performing a database update to our servers on Monday, March 5, beginning at 18:00 UTC. We anticipate that the work will take approximately one hour.
During this time, volunteers will not be able to download new work. No action is required by you, as your devices will automatically retry their connections after the maintenance work is completed.
We appreciate your patience and participation.