From OpenZika via WCG: “Open Zika Researchers Continue Calculations, Share the Wealth, and Spread the Word”

World Community Grid (WCG)

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.

• 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

In total, we have submitted 3.5 billion docking jobs, which involved 427 different target sites. Our initial screens used an older library of 6 million commercially available compounds, and our current experiments utilize a newer library of 30.2 million compounds. We have already received approximately 2.6 billion of these results on our server (there is some lag time between when the calculations are performed on your volunteered machines and when we get the results, since all of the results per “package” of approximately 10,000 – 50,000 different docking jobs need to be returned to World Community Grid, re-organized, and then compressed before sending them to our server).

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!!

Except for a few stragglers, we have received all of the results for our experiments that involve docking 6 million compounds versus NS1, NS3 helicase (both the RNA binding site and the ATP site), and NS5 (both the RNA polymerase and the methyltransferase domains). We are currently receiving the results from our most recent experiments that screen 30.2 million compounds against the NS2B / NS3 protease.

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.

We then ran a quick quality control test to make sure that the software used for the project, AutoDock Vina, could properly use each pdbqt file (a type of docking input file developed by Professor Art Olson’s lab) as an input.

Olson Lab

Many compounds had to be rejected, because they had types of atoms that cause Vina to crash (such as silicon or boron atoms), and we obviously don’t want to waste the computer time that you donate by submitting calculations that will crash.

We then ran a quick quality control test to make sure that the software used for the project, AutoDock Vina, could properly use each pdbqt file (a type of docking input file developed by Professor Art Olson’s lab) as an input. Many compounds had to be rejected, because they had types of atoms that cause Vina to crash (such as silicon or boron atoms), and we obviously don’t want to waste the computer time that you donate by submitting calculations that will crash.

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.

Dr. Melina Mottin presented a lecture entitled “OpenZika: Opening the Discovery of New Antiviral candidates against Zika Virus and Insights into Dynamic behavior of NS3 Helicase”
(Photos taken by Carolina Horta Andrade.)

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

Our PLoS Neglected Tropical Diseases paper, “OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery,” was published on October 20 2016, and it has already been viewed over 4,700 times. Anyone can access and read this paper for free. Another research paper “Illustrating and homology modeling the proteins of the Zika virus” has been formally accepted by F1000Research and viewed > 4,200 times.

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.

These articles are helping to bring additional attention to the project and to encourage the formation of new collaborations. For example, a group from Physics Institute at Sao Carlos, University of Sao Paulo, Brazil, coordinated by Professor Glaucius Oliva, contacted us because of our PLoS Neglected Tropical Diseases paper to discuss a new collaboration to test the selected candidate compounds directly on enzymatic assays with Zika virus proteins. He is the principal investigator for a grant funded by CNPq and FAPESP (Brazilian funding agencies), aiming to clone, express, purify, solve the structure of all the Zika virus proteins, and to develop enzymatic assays to test and identify potential inhibitors. For now, they have already solved a high-resolution (1.9 Å; an Angstrom is a tenth of a nanometer) crystal structure of ZIKV NS5 RNA polymerase (5U04), which has been released on the PDB (Protein Data Bank), and they are working on the determination of new structures of NS3 helicase. We have just started this new collaboration, and the nine selected candidates described earlier in this update are currently being assayed by Prof. Glaucius Oliva and his team to see if they can bind to the NS3 helicase, using the differential scanning fluorescence (DSF) technique and/or if they can inhibit the ATPase activity of this protein.

There is additional news at the full article.

See the full article here.

Ways to access the blog:
https://sciencesprings.wordpress.com
http://facebook.com/sciencesprings

Please help promote STEM in your local schools.

Stem Education Coalition

“World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
WCG projects run on BOINC software from UC Berkeley.

BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

My BOINC

“Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

Please visit the project pages-
Smash Childhood Cancer

FightAIDS@home Phase II

OpenZika

Help Stop TB

Outsmart Ebola together

Mapping Cancer Markers

Uncovering Genome Mysteries

Say No to Schistosoma

GO Fight Against Malaria

Drug Search for Leishmaniasis

Computing for Clean Water

The Clean Energy Project

Discovering Dengue Drugs – Together

Help Cure Muscular Dystrophy

Help Fight Childhood Cancer

Help Conquer Cancer

Human Proteome Folding

FightAIDS@Home

World Community Grid is a social initiative of IBM Corporation
IBM Corporation

IBM – Smarter Planet

From WCG: “New Lab at Tsinghua University Created to Work on Computing for Clean Water Project Findings”

World Community Grid (WCG)

25 Jul 2017
The Computing for Clean Water team

Summary
Dr. Ming Ma, one of the original members of the Computing for Clean Water research team, has created his own lab at Tsinghua University. Dr. Ma and his team continue to analyze the data generated by the project. Learn more about their current work and plans for the future in this update.

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 team at Tsinghua University includes (left to right) Ming Ma, Kunqi Wang, Wei Cao, and Jin Wang. Not pictured: Yao Cheng

A Growing Team

It has been one year since the main team member, Dr. Ming Ma, returned to Tsinghua University, China, after doing research at University College London and Tel Aviv University. During the past year, as an Associate Professor in the Department of Mechanical Engineering, Dr. Ma recruited four new researchers as members of the team with the help from Prof. Quanshui Zheng, the leader of the Computing for Clean Water team. The new team members include one postdoc, Dr. Wei Cao; and three PhD students: Jin Wang, Kunqi Wang, and Yao Cheng.

Next Steps

The team is now working on two main tasks. The first task is to improve the algorithm used in the previous study (see the reference below) by incorporating new techniques developed during the last three years, and to implement them into LAMMPS, a molecular dynamics software. The second task is to investigate new systems with the algorithm being developed. With these tasks finished, the team wishes to bring new, interesting information into the volunteer computing community.

We thank everyone who supported Computing for Clean Water, and hope to work with you again in the near future.

Reference

M. Ma, F. Grey, L.M. Shen, M. Urbakh, S. Wu, J.Z. Liu, Y.L. Liu, Q.S. Zheng, Water transport inside carbon nanotubes mediated by phonon-induced oscillating friction, Nature Nanotech., 10 (2015) 692-695

See the full article here.

Ways to access the blog:
https://sciencesprings.wordpress.com
http://facebook.com/sciencesprings

Please help promote STEM in your local schools.

Stem Education Coalition

“World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
WCG projects run on BOINC software from UC Berkeley.

BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

My BOINC

“Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

Please visit the project pages-

FightAIDS@home Phase II

OpenZika

Help Stop TB

Outsmart Ebola together

Mapping Cancer Markers

Uncovering Genome Mysteries

Say No to Schistosoma

GO Fight Against Malaria

Drug Search for Leishmaniasis

Computing for Clean Water

The Clean Energy Project

Discovering Dengue Drugs – Together

Help Cure Muscular Dystrophy

Help Fight Childhood Cancer

Help Conquer Cancer

Human Proteome Folding

FightAIDS@Home

World Community Grid is a social initiative of IBM Corporation
IBM Corporation

IBM – Smarter Planet

From Scripps: “Scientists Jump Hurdle in HIV Vaccine Design”

Scripps Research Institute

June 19, 2017 issue
Madeline McCurry-Schmidt

The new study shows the structure of an important HIV protein, called the envelope glycoprotein, on a common strain of the virus. (Image courtesy Javier Guenaga.)

Scientists at The Scripps Research Institute (TSRI) have made another important advance in HIV vaccine design. The development was possible thanks to previous studies at TSRI showing the structures of a protein on HIV’s surface, called the envelope glycoprotein. The scientists used these structures to design a mimic of the viral protein from a different HIV subtype, subtype C, which is responsible for the majority of infections worldwide.

The new immunogen is now part of a growing library of TSRI-designed immunogens that could one day be combined in a vaccine to combat many strains of HIV.

“All of this research is going toward finding combinations of immunogens to aid in protecting people against HIV infection,” said TSRI Professor Ian Wilson, Hanson Professor of Structural Biology and chair of the Department of Integrative Structural and Computational Biology at TSRI.

The research, published recently in the journal Immunity, was led by Wilson and TSRI Professor of Immunology Richard Wyatt, who also serves as Director of Viral Immunology for the International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center at TSRI.

The new study was published alongside a second study in Immunity, led by scientists at the Karolinska Institute in Stockholm, which showed that the vaccine candidate developed in the TSRI-led study can elicit neutralizing antibodies in non-human primates.

“Together, the two studies reiterate how structure-based immunogen design can advance vaccine development,” said Wyatt.

Solving the Clade C Structure

HIV mutates rapidly, so there are countless strains of HIV circulating around the world. Of these strains, scientists tend to focus on the most common threats, called clades A, B and C.

Like a flu vaccine, an effective HIV vaccine needs to protect against multiple strains, so researchers are designing a set of immunogens that can be given sequentially or as a cocktail to people so their immune systems can prepare for whatever strain they come up against.

In 2013, TSRI scientists, led by Wilson and TSRI Associate Professor Andrew Ward, determined the structure of a clade A envelope glycoprotein, which recognizes host cells and contains the machinery that HIV uses to fuse with cells. Because this is the only antibody target on the surface of HIV, an effective HIV vaccine will have to trigger the body to produce antibodies to neutralize the virus by blocking these activities.

Building on the previous original research, the scientists in the new study set out to solve the structure of the clade C glycoprotein and enable the immune system to fight clade C viruses.

“Clade C is the most common subtype of HIV in sub-Saharan Africa and India,” explained study co-first author Javier Guenaga, an IAVI collaborator working at TSRI. “Clade C HIV strains are responsible for the majority of infections worldwide.”

The scientists faced a big challenge: the clade C envelope glycoprotein is notoriously unstable, and the molecules are prone to falling apart.

Guenaga needed the molecules to stay together as a trimer so his co-author Fernando Garces could get a clear image of the clade C glycoprotein’s trimeric structure. To solve this problem, Guenaga re-engineered the glycoprotein and strengthened the interactions between the molecules. “We reinforced the structure to get the soluble molecule to assemble as it is on the viral surface,” Guenaga said.

The project took patience, but it paid off. “Despite all the engineering employed to produce a stable clade C protein, these crystals (of clade C protein) were grown in very challenging conditions at 4 degrees Celsius and it took the diffraction of multiple crystals to generate a complete dataset, as they showed high sensitivity to radiation damage,” said Garces. “Altogether, this highlights the tremendous effort made by the team in order to make available the molecular architecture of this very important immunogen.”

With these efforts, the glycoprotein could then stay together in solution the same way it remains together on the virus itself. The researchers then captured a high-resolution image of the glycoprotein using a technique called x-ray crystallography.

The researchers finally had a map of the clade C glycoprotein.

Vaccine Candidate Shows Promise

In a companion study, the scientists worked with a team at the Karolinska Institute to test an immunogen based on Guenaga’s findings. The immunogen was engineered to appear on the surface of a large molecule called a liposome—creating a sort of viral mimic, like a mugshot of the virus.

This vaccine candidate indeed prompted the immune system to produce antibodies that neutralized the corresponding clade C HIV strain when tested in non-human primates.

“That was great to see,” said Guenaga. “This study showed that the immunogens we made are not artificial molecules—these are actually relevant for protecting against HIV in the real world.”

In addition to Wyatt, Wilson and Guenaga, the study, “Glycine substitution at helix-to-coil transitions facilitates the structural determination of a stabilized subtype C HIV envelope glycoprotein,” included co-first author Fernando Garces, Natalia de Val, Viktoriya Dubrovskaya and Brett Higgins of TSRI; Robyn L. Stanfield of TSRI and IAVI; Barbara Carrette of IAVI; and Andrew Ward of TSRI, IAVI and the Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery (CHAVI-ID) at TSRI.

This work was supported by the IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD; grants OPP1084519 and OPP1115782), CHAVI-ID (grant UM1 AI00663) and the National Institutes of Health (grants P01 HIVRAD AI104722, R56 AI084817 and U54 GM094586).

See the full article here .

YOU CAN HELP IN THE FIGHT AGAINST HIV/AIDS FROM THE COMFORT OF YOUR EASY CHAIR.

The Fight AIDS at home (FAAH@home) Phase II project is now running at World Community Grid (WCG) From Scripps Research Institute.

WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the FAAH@home Phase II project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.

My BOINC

Please help promote STEM in your local schools.

Stem Education Coalition

The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

From NIH: “Antibodies from Ebola survivor could lead to treatments and vaccines”

National Institutes of Health

June 6, 2017
Harrison Wein, Ph.D.

Colorized scanning electron micrograph of filamentous Ebola virus particles (green) attached to and budding from an infected cell (blue) (25,000x magnification).NIAID

The 2013-16 Ebola outbreak in West Africa highlighted the need for an effective treatment or vaccine. Researchers have been making progress on several fronts, but many scientific and logistical challenges loom.

Viruses from three of the five known ebolavirus species (Zaire, Sudan, and Bundibugyo) have caused large outbreaks in humans, and the other two (Reston and Tai Forest) cause severe disease in primates. The related Marburg and Ravn viruses also cause similar hemorrhagic fevers and serious outcomes in people. An ideal approach would target many, if not all, of the viruses in this family, called filoviruses.

Scientists have searched for insights from natural antibodies, molecules produced by the immune system that bind to a specific substance, such as an invading virus. Antibodies recognize small, often unique, portions of viruses. Researchers previously discovered an antibody from a mouse that recognizes a common region among multiple ebolavirus species. The antibody proved protective in mouse models of infection.

A team of academic, industry, and government scientists set out to find similar broadly protective human antibodies. The group was led by Dr. John M. Dye at the U.S. Army Medical Research Institute of Infectious Diseases, Dr. Kartik Chandran at Albert Einstein College of Medicine, and Dr. Zachary A. Bornholdt at Mapp Biopharmaceutical, Inc. Their work was funded in part by NIH’s National Institute of Allergy and Infectious Diseases (NIAID). Results appeared in Cell on May 18, 2017.

The researchers surveyed 349 antibodies derived from the blood of one survivor of the West African Ebola outbreak, which was caused by the Zaire strain of ebolavirus. They searched for antibodies that could neutralize all five ebolavirus species. Two that they found of interest were called ADI-15878 and ADI-15742. Both protected human cells in the laboratory from becoming infected with the three ebolaviruses that cause outbreaks in humans. Neither, however, protected against the more distantly related filoviruses Lloviu or Marburg.

In animal models of ebolavirus infection, the antibodies protected mice from the Zaire and Sudan ebolaviruses and ferrets from Bundibugyo ebolavirus. However, in ferrets treated with ADI-15742, the researchers found that the virus had developed a mutation that enabled it to escape the antibody’s effects.

Further study showed that the antibodies recognize a section of a protein found on the surface of ebolaviruses called the GP fusion loop, which is critical for infection. The antibodies don’t prevent the viruses from being engulfed by cells. Rather, they are taken up along with the virus particles and neutralize the viruses as they are being processed within the cell.

“Since it’s impossible to predict which of these agents will cause the next epidemic, it would be ideal to develop a single therapy that could treat or prevent infection caused by any known ebolavirus,” Bornholdt says. While much work still needs to be done, the identification of this vulnerable shared region on the surface of ebolaviruses is an important step toward creating effective treatments or vaccines.

See the full article here .

You can Help Stamp Out EBOLA.

This WCG project runs at Scripps Institute

Visit World Community Grid (WCG). Download and install the BOINC software on which it runs. Attach to the Outsmart Ebola Together project. This will allow WCG to use your computer’s free CPU cycles to process computational data for the project.

While you are at WCG and BOINC, check out the other very worthwhile projects running on this software. All project results are “open source”, free for the use of scientists world while to advance health and other issues of mankind.

Please help promote STEM in your local schools.

Stem Education Coalition

The National Institutes of Health (NIH), a part of the U.S. Department of Health and Human Services, is the nation’s medical research agency — making important discoveries that improve health and save lives.

From BOINC project SixTrack: 2017 pentathlon hosted by SETI.Germany

BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing, developed at UC Berkeley.

LHC Sixtrack

The SixTrack team would like to thank all the teams who took part in the 2017 pentathlon hosted by SETI.Germany:
https://www.seti-germany.de/boinc_pentathlon/
where LHC@Home was chosen for the swimming discipline. The pentathlon gave us the possibility of carrying out a vast simulation campaign, with lots of new results generated that we are now analysing. While the LHC experiments send volunteers tasks where data collected by the LHC detectors has to be analysed or Monte Carlo codes for data generation, SixTrack work units probe the dynamics of LHC beams; hence, your computers are running a live model of the LHC in order to explore its potential without actually using real LHC machine time, precious to physics.

SixTRack CERN LHC particles

Your contribution to our analyses is essential. For instance, we reached ~2.5 MWUs processed in total, with a peak slightly above 400kWUs processed at the same time, and >50TFLOPs, during the entire two weeks of the pentathlon. The pentathlon was also the occasion to verify recent improvements to our software infrastructure. After this valuable experience, we are now concentrating our energies on updating the executables with brand new functionality, extending the range of studies and of supported systems. This implies an even increased dependence on your valuable support.

Thanks a lot to all people involved! We count on your help and committment to science and to LHC@home to pursue the new challenges of beam dynamics which lie ahead.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

Visit the BOINC web page, click on Choose projects and check out some of the very worthwhile studies you will find. Then click on Download and run BOINC software/ All Versons. Download and install the current software for your 32bit or 64bit system, for Windows, Mac or Linux. When you install BOINC, it will install its screen savers on your system as a default. You can choose to run the various project screen savers or you can turn them off. Once BOINC is installed, in BOINC Manager/Tools, click on “Add project or account manager” to attach to projects. Many BOINC projects are listed there, but not all, and, maybe not the one(s) in which you are interested. You can get the proper URL for attaching to the project at the projects’ web page(s) BOINC will never interfere with any other work on your computer.

My BOINC

MAJOR PROJECTS RUNNING ON BOINC SOFTWARE

SETI@home The search for extraterrestrial intelligence. “SETI (Search for Extraterrestrial Intelligence) is a scientific area whose goal is to detect intelligent life outside Earth. One approach, known as radio SETI, uses radio telescopes to listen for narrow-bandwidth radio signals from space. Such signals are not known to occur naturally, so a detection would provide evidence of extraterrestrial technology.

Radio telescope signals consist primarily of noise (from celestial sources and the receiver’s electronics) and man-made signals such as TV stations, radar, and satellites. Modern radio SETI projects analyze the data digitally. More computing power enables searches to cover greater frequency ranges with more sensitivity. Radio SETI, therefore, has an insatiable appetite for computing power.

Previous radio SETI projects have used special-purpose supercomputers, located at the telescope, to do the bulk of the data analysis. In 1995, David Gedye proposed doing radio SETI using a virtual supercomputer composed of large numbers of Internet-connected computers, and he organized the SETI@home project to explore this idea. SETI@home was originally launched in May 1999.”

SETI@home is the birthplace of BOINC software. Originally, it only ran in a screensaver when the computer on which it was installed was doing no other work. With the powerand memory available today, BOINC can run 24/7 without in any way interfering with other ongoing work.

The famous SET@home screen saver, a beauteous thing to behold.

einstein@home The search for pulsars. “Einstein@Home uses your computer’s idle time to search for weak astrophysical signals from spinning neutron stars (also called pulsars) using data from the LIGO gravitational-wave detectors, the Arecibo radio telescope, and the Fermi gamma-ray satellite. Einstein@Home volunteers have already discovered more than a dozen new neutron stars, and we hope to find many more in the future. Our long-term goal is to make the first direct detections of gravitational-wave emission from spinning neutron stars. Gravitational waves were predicted by Albert Einstein almost a century ago, but have never been directly detected. Such observations would open up a new window on the universe, and usher in a new era in astronomy.”

MilkyWay@Home Milkyway@Home uses the BOINC platform to harness volunteered computing resources, creating a highly accurate three dimensional model of the Milky Way galaxy using data gathered by the Sloan Digital Sky Survey. This project enables research in both astroinformatics and computer science.”

Leiden Classical “Join in and help to build a Desktop Computer Grid dedicated to general Classical Dynamics for any scientist or science student!”

World Community Grid (WCG) World Community Grid is a special case at BOINC. WCG is part of the social initiative of IBM Corporation and the Smarter Planet. WCG has under its umbrella currently eleven disparate projects at globally wide ranging institutions and universities. Most projects relate to biological and medical subject matter. There are also projects for Clean Water and Clean Renewable Energy. WCG projects are treated respectively and respectably on their own at this blog. Watch for news.

Rosetta@home “Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s….”

GPUGrid.net “GPUGRID.net is a distributed computing infrastructure devoted to biomedical research. Thanks to the contribution of volunteers, GPUGRID scientists can perform molecular simulations to understand the function of proteins in health and disease.” GPUGrid is a special case in that all processor work done by the volunteers is GPU processing. There is no CPU processing, which is the more common processing. Other projects (Einstein, SETI, Milky Way) also feature GPU processing, but they offer CPU processing for those not able to do work on GPU’s.

These projects are just the oldest and most prominent projects. There are many others from which you can choose.

There are currently some 300,000 users with about 480,000 computers working on BOINC projects That is in a world of over one billion computers. We sure could use your help.

From The Atlantic via SETI@home: “A Brief History of SETI@Home”

SETI@home

The Atlantic

Frank Drake, (Left) president of the SETI (Search for Extraterrestrial Intelligence) reviews data from radiotelescopes used to scan the universe for intelligent life.

How astronomers deputized early internet users to help find alien civilizations.

The year was 1999, and the people were going online. AOL, Compuserve, mp3.com, and AltaVista loaded bit by bit after dial-up chirps, on screens across the world. Watching the internet extend its reach, a small group of scientists thought a more extensive digital leap was in order, one that encompassed the galaxy itself. And so it was that before the new millennium dawned, researchers at the University of California released a citizen-science program called SETI@Home.

The idea went like this: When internet-farers abandoned their computers long enough that a screen saver popped up, that saver wouldn’t be WordArt bouncing around, 3-D neon-metallic pipes installing themselves inch by inch, or a self-satisfied flying Windows logo. No. Their screens would be saved by displays of data analysis, showing which and how much data from elsewhere their CPUs were churning through during down-time. The data would come from observations of distant stars, conducted by astronomers searching for evidence of an extraterrestrial intelligence. Each participating computer would dig through SETI data for suspicious signals, possibly containing a “Hello, World” or two from aliens. Anyone with 28 kbps could be the person to discover another civilization.

When the researchers launched SETI@Home, in May of ’99, they thought maybe 1,000 people might sign up. That number—and the bleaker view from outsiders, who said perhaps no one would join the crew—informed a poor decision: to set up a single desktop to farm out the data and take back the analysis.

But the problem was, people really liked the idea of letting their computers find aliens while they did nothing except not touch the mouse. And for SETI@Home’s launch, a million people signed up. Of course, the lone data-serving desktop staggered. SETI@Home fell down as soon as it started walking. Luckily, now-defunct Sun Microsystems donated computers to help the program get back on its feet. In the years since, more than 4 million people have tried SETI@Home. Together, they make up a collective computing power that exceeds 2008’s premier supercomputer.

But they have yet to find any aliens.

SETI is a middle-aged science, with 57 years under its sagging belt. It began in 1960, when an astronomer named Frank Drake used an 85-foot radio telescope in Green Bank, West Virginia, to scan two Sun-like stars for signs of intelligent life—radio emissions the systems couldn’t produce on their own, like the thin-frequency broadcasts of our radio stations, or blips that repeated in a purposeful-looking way.

Green Bank today

GBO radio telescope, Green Bank, West Virginia, USA

Since then, scientists and engineers have used radio and optical telescopes to search much more of the sky—for those “narrowband” broadcasts, for fast pings, for long drones, for patterns distinguishing themselves from the chaotic background static and natural signals from stars and supernovae.

But the hardest part about SETI is that scientists don’t know where ET may live, or how ET’s civilization might choose to communicate. And so they have to look for a rainbow of possible missives from other solar systems, all of which move and spin at their own special-snowflake speeds through the universe. There’s only one way to do that, says Dan Werthimer, the chief SETI scientist at Berkeley and a co-founder of SETI@Home: “We need a lot of computing power.”

In the 1970s, when Werthimer’s Berkeley colleagues launched a SETI project called SERENDIP, they sucked power from all the computers in their building, then the neighboring building. In a way, it was a SETI@Home prototype. In the decades that followed, they turned to supercomputers. And then, they came for your CPUs.

The idea for SETI@Home originated at a cocktail party in Seattle, when computer scientist David Gedye asked a friend what it might take to excite the public about science. Could computers somehow do something similar to what the Apollo program had done? Gedye dreamed up the idea of “volunteer computing,” in which people gave up their hard drives for the greater good when those drives were idle, much like people give up their idle cars, for periods of time, to Turo (if Turo didn’t make money and also served the greater good). What might people volunteer to help with? His mind wandered to The X-Files, UFOs, hit headlines fronting the National Enquirer. People were so interested in all that. “It’s a slightly misguided interest, but still,” says David Anderson, Gedye’s graduate-school advisor at Berkeley. Interest is interest is interest, misguided or guided perfectly.

But Gedye wasn’t a SETI guy—he was a computer guy—so he didn’t know if or how a citizen-computing project would work. He got in touch with astronomer Woody Sullivan, who worked at the University of Washington in Seattle. Sullivan turned him over to Werthimer. And Gedye looped in Anderson. They had a quorum, of sorts.

Anderson, who worked in industry at the time, dedicated evenings to writing software that could take data from the Arecibo radio telescope, mother-bird it into digestible bits, send it to your desktop, command it to hunt for aliens, and then send the results back to the Berkeley home base. No small task.

They raised some money—notably, $50,000 from the Planetary Society and $10,000 from a Paul Allen-backed company. But most of the work-hours, like the computer-hours they were soliciting, were volunteer labor. Out of necessity, they did hire a few people with operating-system expertise, to deal with the wonky screensaver behavior of both Windows and Macintosh. “It’s difficult trying to develop a program that’s intended to run on every computer in the world,” says Anderson.

__________________________________________________________________
Today, you can use BOINC to serve up your computer’s free time to develop malaria drugs, cancer drugs, HIV drugs.

__________________________________________________________________

And yet, by May 17, 1999, they were up, and soon after, they were running. And those million people in this world were looking for not-people on other worlds.

One morning, early in the new millennium, the team came into the office and surveyed the record of what those million had done so far. In the previous 24 hours, the volunteers had done what would have taken a single desktop one thousand years to do. “Suppose you’re a scientist, and you have some idea, and it’s going to take 1,000 years,” says Anderson. “You’re going to discard it. But we did it.”

After being noses-down to their keyboards since the start, it was their first feeling of triumph. “It was really a battle for survival,” says Anderson. “We didn’t really have time to look up and realize what an amazing thing we were doing.”

Then, when they looked up again, at the SETI@Home forums, they saw something else: “It was probably less than a year after we started that we started getting notices about the weddings of people who met through SETI@Home,” says Eric Korpela, a SETI@Home project scientist and astronomer at Berkeley.

The SETI astronomers began to collect more and different types of data, from the likes of the Arecibo radio telescope. Operating systems evolved. There were new signal types to search for, like pulses so rapid they would have seemed like notes held at pianissimo to previous processors. With all that change, they needed to update the software frequently. But they couldn’t put out a new version every few months and expect people to download it.

Anderson wanted to create a self-updating infrastructure that would solve that problem—and be flexible enough that other, non-SETI projects could bring their work onboard and benefit from distributed computing. And so BOINC—Berkeley Open Infrastructure for Network Computing—was born.

Today, you can use BOINC to serve up your computer’s free time to develop malaria drugs, cancer drugs, HIV drugs. You can fold proteins or help predict the climate. You can search for gravitational waves or run simulations of the heart’s electrical activity, or any of 30 projects. And you can now run BOINC on GPUs—graphical processing units, brought to you by gamers—and on Android smartphones Nearly half a million people use the infrastructure now, making the système totale a 19 petaflop supercomputer, the third-largest megacalculator on the planet.

Home computers have gotten about 100 times faster since 1999, thank God, and on the data distribution side, Berkeley has gotten about 10 times faster. They’re adding BOINC as a bandwidth-increasing option to the Texas Advanced Computing Center and nanoHUB, and also letting people sign up for volunteer computing, tell the system what they think are the most important scientific goals, and then have their computers be automatically matched to projects as those projects need time. It’s like OkCupid dating, for scientific research. BOINC, and SETI@Home can do more work than ever.

The thing is, though, they’ve already done a lot of work—so much work they can’t keep up with themselves. Sitting in a database are 7 billion possible alien signals that citizen scientists and their idle computers have already uncovered.

Most of these are probably human-made interference: short-circuiting electric fences, airport radar, XM satellite radio, or a microwave opened a second too soon. Others are likely random noise that added up to a masquerade of significance. As Anderson says, “Random noise has the property that whatever you’re looking for, it eventually occurs. If you generate random letters. You eventually get the complete works of Shakespeare.” Or the emissions are just miscategorized natural signals.

Anderson has been working on a program called Nebula that will trawl that billions-and-billions-strong database, reject the interference, and upvote the best candidates that might—just might—be actual alien signals. Four thousand computers at the Max Planck Institute for Gravitational Physics in Germany help him narrow down the digital location of that holiest of grails. Once something alien in appearance pops up—say from around the star Vega—the software automatically searches the rest of the data. It finds all the other times, in the 18 years of SETI@Home history, that Arecibo or the recently added telescopes from a $100 milion initiative called Breakthrough Listen have looked at Vega. Was the signal there then too? “We’re kind of hoping that the aliens are sending a constant beacon,” says Korpela, “and that every time a telescope passes over a point in the sky, we see it.”

If no old data exists—or if the old data is particularly promising—the researchers request new telescope time and ask SETI colleagues to verify the signal with their own telescopes, to see if they can intercept that beacon, that siren, that unequivocal statement of what SETI scientists and SETI@Home participants hope is true: That we are not alone.

So far, that’s a no-go. “We’ve never had a candidate so exciting that we call the director and say, ‘Throw everybody off the telescope,’” says Werthimer. “We’ve never had anything that resembles ET.”

And partly for that reason, the SETI@Homers are now working on detecting “wideband” signals—ones that come at a spread spectrum of frequencies, like the beam-downs from DIRECTV. Humans (and by extension, extraterrestrials) can embed more information more efficiently in these spread-spectrum emissions. If the goal is to disseminate information, rather than just graffiti “We’re here!” on the fabric of spacetime, wideband is the way to go. And SETI scientists’ thinking goes like this: We’ve been looking mostly for purposeful, obvious transmissions, ones wrapped neatly for us. But we haven’t found any—which might mean they just aren’t there. Extraterrestrial communications might be aimed at members of their own civilizations, in which case they’re more likely to go the DIRECTV route, and we’re likely to find only the “leakage” of those communication lines.

“If there really are these advanced civilizations, it’d be trivial to contact us,” says Werthimer. “They’d be landing on the White House—well, maybe not this White House. But they’d be shining a laser in Frank Drake’s eyes. I don’t see why they would make it so difficult that we would have to do all this hard stuff.”

And so humans, and our sleeping computers, may have to eavesdrop on messages not addressed to us—the ones the aliens send to their own (for lack of a better word) people, and then insert ourselves into the chatter. “I don’t mean to interrupt,” we might someday say, “but I couldn’t help overhearing…” And because of SETI@Home and BOINC, it might be your laptop that gets that awkward conversation started.

See the full article here.

Please help promote STEM in your local schools.

Stem Education Coalition

The science of SETI@home
SETI (Search for Extraterrestrial Intelligence) is a scientific area whose goal is to detect intelligent life outside Earth. One approach, known as radio SETI, uses radio telescopes to listen for narrow-bandwidth radio signals from space. Such signals are not known to occur naturally, so a detection would provide evidence of extraterrestrial technology.

Radio telescope signals consist primarily of noise (from celestial sources and the receiver’s electronics) and man-made signals such as TV stations, radar, and satellites. Modern radio SETI projects analyze the data digitally. More computing power enables searches to cover greater frequency ranges with more sensitivity. Radio SETI, therefore, has an insatiable appetite for computing power.

Previous radio SETI projects have used special-purpose supercomputers, located at the telescope, to do the bulk of the data analysis. In 1995, David Gedye proposed doing radio SETI using a virtual supercomputer composed of large numbers of Internet-connected computers, and he organized the SETI@home project to explore this idea. SETI@home was originally launched in May 1999.

SETI@home is not a part of the SETI Institute

The SETI@home screensaver image

To participate in this project, download and install the BOINC software on which it runs. Then attach to the project. While you are at BOINC, look at some of the other projects which you might find of interest.

MAJOR PROJECTS RUNNING ON BOINC SOFTWARE

SETI@home The search for extraterrestrial intelligence. “SETI (Search for Extraterrestrial Intelligence) is a scientific area whose goal is to detect intelligent life outside Earth. One approach, known as radio SETI, uses radio telescopes to listen for narrow-bandwidth radio signals from space. Such signals are not known to occur naturally, so a detection would provide evidence of extraterrestrial technology.

Radio telescope signals consist primarily of noise (from celestial sources and the receiver’s electronics) and man-made signals such as TV stations, radar, and satellites. Modern radio SETI projects analyze the data digitally. More computing power enables searches to cover greater frequency ranges with more sensitivity. Radio SETI, therefore, has an insatiable appetite for computing power.

Previous radio SETI projects have used special-purpose supercomputers, located at the telescope, to do the bulk of the data analysis. In 1995, David Gedye proposed doing radio SETI using a virtual supercomputer composed of large numbers of Internet-connected computers, and he organized the SETI@home project to explore this idea. SETI@home was originally launched in May 1999.”

SETI@home is the birthplace of BOINC software. Originally, it only ran in a screensaver when the computer on which it was installed was doing no other work. With the powerand memory available today, BOINC can run 24/7 without in any way interfering with other ongoing work.

The famous SET@home screen saver, a beauteous thing to behold.

einstein@home The search for pulsars. “Einstein@Home uses your computer’s idle time to search for weak astrophysical signals from spinning neutron stars (also called pulsars) using data from the LIGO gravitational-wave detectors, the Arecibo radio telescope, and the Fermi gamma-ray satellite. Einstein@Home volunteers have already discovered more than a dozen new neutron stars, and we hope to find many more in the future. Our long-term goal is to make the first direct detections of gravitational-wave emission from spinning neutron stars. Gravitational waves were predicted by Albert Einstein almost a century ago, but have never been directly detected. Such observations would open up a new window on the universe, and usher in a new era in astronomy.”

MilkyWay@Home Milkyway@Home uses the BOINC platform to harness volunteered computing resources, creating a highly accurate three dimensional model of the Milky Way galaxy using data gathered by the Sloan Digital Sky Survey. This project enables research in both astroinformatics and computer science.”

Leiden Classical “Join in and help to build a Desktop Computer Grid dedicated to general Classical Dynamics for any scientist or science student!”

World Community Grid (WCG) World Community Grid is a special case at BOINC. WCG is part of the social initiative of IBM Corporation and the Smarter Planet. WCG has under its umbrella currently eleven disparate projects at globally wide ranging institutions and universities. Most projects relate to biological and medical subject matter. There are also projects for Clean Water and Clean Renewable Energy. WCG projects are treated respectively and respectably on their own at this blog. Watch for news.

Rosetta@home “Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s….”

GPUGrid.net “GPUGRID.net is a distributed computing infrastructure devoted to biomedical research. Thanks to the contribution of volunteers, GPUGRID scientists can perform molecular simulations to understand the function of proteins in health and disease.” GPUGrid is a special case in that all processor work done by the volunteers is GPU processing. There is no CPU processing, which is the more common processing. Other projects (Einstein, SETI, Milky Way) also feature GPU processing, but they offer CPU processing for those not able to do work on GPU’s.

These projects are just the oldest and most prominent projects. There are many others from which you can choose.

There are currently some 300,000 users with about 480,000 computers working on BOINC projects That is in a world of over one billion computers. We sure could use your help.

My BOINC

From WCG: Ebola outbreak

World Community Grid (WCG)

The World Health Organization just announced three recent deaths from Ebola in the Democratic Republic of Congo, which may grown into a new outbreak of the disease. Please support the Outsmart Ebola Together project and help scientists find better treatments for this deadly virus.

Outsmart Ebola Together

You can help researchers at The Scripps Research Institute find a cure for Ebola by donating your computing power to this project and encouraging others to join.

You can also support the research team by contributing to The Scripps Research Institute’s crowdfunding campaign. The team will use these funds to analyze the enormous volume of data generated by Outsmart Ebola Together and study the most promising drug candidates.

The Ebola virus is a significant global health threat and is a growing humanitarian crisis in Africa, killing thousands of victims in 2014.

http://www.webmd.com/a-to-z-guides/ebola-fever-virus-infection

If not handled properly, an Ebola outbreak can turn into an epidemic, overwhelming regional health services and disrupting trade and the delivery of social services, causing the welfare and economy of a region to deteriorate. The ongoing viral load in the human population increases the likelihood of further mutation. Additionally, the virus’s long incubation period and our highly connected modern world could allow the virus to spread to new geographies and across oceans.

Currently, there are no approved treatments or vaccines for this deadly disease, and the search for an effective antiviral drug to treat the disease is a high priority. While previous outbreaks have ended when the disease disappeared from the human population, the scope of the 2014 outbreak raises the possibility that the virus, rather than disappearing again, could become endemic – permanently persisting in human populations in one or more areas.

Outsmart Ebola Together on World Community Grid aims to help researchers at The Scripps Research Institute develop a treatment for Ebola virus. The computational power donated by World Community Grid volunteers is being used to screen millions of candidate drug molecules to identify ones that can disable the Ebola virus.

See the full article here.

Ways to access the blog:
https://sciencesprings.wordpress.com
http://facebook.com/sciencesprings

Please help promote STEM in your local schools.

Stem Education Coalition

“World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
WCG projects run on BOINC software from UC Berkeley.

BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

My BOINC

“Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

Please visit the project pages-

FightAIDS@home Phase II

OpenZika

Help Stop TB

Outsmart Ebola together

Mapping Cancer Markers

Uncovering Genome Mysteries

Say No to Schistosoma

GO Fight Against Malaria

Drug Search for Leishmaniasis

Computing for Clean Water

The Clean Energy Project

Discovering Dengue Drugs – Together

Help Cure Muscular Dystrophy

Help Fight Childhood Cancer

Help Conquer Cancer

Human Proteome Folding

FightAIDS@Home

World Community Grid is a social initiative of IBM Corporation
IBM Corporation

IBM – Smarter Planet

From Mapping Cancer Markers at WCG: “Mapping Cancer Markers Team Analyzes Lung Cancer Data”

World Community Grid (WCG)

By: The Mapping Cancer Markers research team
6 Apr 2017

Summary
In this project update, the Mapping Cancer Markers team describes how they are analyzing 45 million of the most promising lung cancer data results, and how they have begun to disseminate their early findings.

The Mapping Cancer Markers (MCM) project continues to process work units for the Ovarian Cancer dataset. As we accumulate these results, we continue to analyze MCM results from the previous Lung Cancer dataset. Below, we discuss one direction in which we are pursuing the analysis.

Patterns of gene-family signatures in lung cancer

In cancer, and human biology in general, multiple biomarkers (genes, proteins, microRNAs, etc.) can have similar patterns of activity. This may be because the genes serve redundant roles, or because the genes (or other molecules) participate together in a group to serve a biological function. A cancer signature composed of a set of specific genes may appear different than another signature composed of different, specific genes, and yet perform equivalently because the genes in each are functionally related. With this problem in mind, post-doctorate fellow Anne-Christin Hauschild is leading a study of frequently-occurring patterns (or motifs) of genes present in high-performing lung cancer gene signatures.

Illustration 1: Summary of the analysis workflow

This project looked at the first phase results from the Lung Cancer MCM analysis, which was a systematic exploration of the entire space of potential fixed-length signatures. We began by selecting 45 million high-performing signatures derived from World-Community-Grid-computed MCM results. These are the signatures evaluated to carry the most information for lung cancer diagnosis.

Next, we divided all genes in the lung cancer dataset into 180 clusters (gene families), where genes in each family show similar activity in the lung cancer dataset. We then labelled those top signatures with the gene families into which the genes were assigned. This gave us a set of high-performing signatures expressed as gene families instead of genes. This allowed us to treat two different gene signatures as the same gene-family signature, as long as the corresponding genes in each signature are members of the same family.

To help understand the gene-families themselves, we can visualize each one with word clouds that describe the functions of the genes they contain, or the biological pathways they represent. We draw this information from databases such as Gene Ontology, pathDIP, or other sources.

From there, we looked for patterns in these gene-family signatures: which families appear unusually frequently (or rarely) in high-performing signatures, or families that tend to appear multiple times in the same signature. We used Frequent-Itemset mining algorithm to discover specific patterns that occur unusually frequently in good signatures.

Illustration 2: Some gene families occur multiple times in a single signature with surprising frequency (high or low). Family 109 rarely appears multiple times. Family 12 appears surprisingly often in 9x multiples.

Illustration 3: Several important gene families, characterized by word clouds describing the genes’ molecular function annotations from the Gene Ontology database. Circles group families into common patterns found in high-performing signatures. Patterns often overlap, as in this example: one pattern containing families 3, 5, and 18 intersects with another containing families 12, 18, and 57.

Using databases such as IID or pathDIP, we can take these patterns and examine the relationships between the gene-families they contain, so we can start to understand why certain combinations of such families carry so much information about lung cancer. We use NAViGaTOR to visualize and explore these complex sets of relationships.

Illustration 4: Relationship between 11 significant gene families (large circles) within a protein interaction network. Only the most important genes (dots, colour-coded by biological function) in each family are shown.

We presented the preliminary results of this project to Canadian and international cancer researchers this February, in a poster at the Personalizing Cancer Medicine Conference 2017 in Toronto, Ontario. We gained many insights and ideas from discussing this early work, and we continue developing them further.

Some of the additional, related results have been presented in other publications, including:

Pinheiro, M., Drigo, S.A., Tonhosolo, R., Andrade, S.C.S., Marchi, F.A., Jurisica, I., Kowalski, L.P., Achatz, M.I., Rogatto, S.R., HABP2 p.G534E variant in patients with family history of thyroid and breast cancer, Oncotarget, In press.
Citron, F., Armenia, J., Barzan, L., Franchin, G., Polesel, J., Talamini, R., Sulfaro, S., Croce, C.M., Klement, W., Pastrello, C., Jurisica, I., Vecchione, A., Belletti, B., Baldassarre, G., A microRNA signature identifies SP1 and TGFbeta pathways as potential mediators of local recurrences in head and neck squamous carcinomas, Clin Cancer Res, In press.
Sokolina K, Kittanakom S, Snider J, Kotlyar M, Maurice P, Gandía J, Benleulmi-Chaachoua A, Tadagaki K, Wong V, Malty RH, Deineko V, Aoki H, Amin S, Riley L, Yao Z, Morató X, Otasek D, Kobayashi H, Menendez J, Auerbach D, Angers S, Pržulj N, Bouvier M, Babu M, Ciruela F, Jockers R, Jurisica I, and Stagljar I. Systematic protein-protein interaction mapping for clinically-relevant human GPCRs, Mol Sys Biol, In press.
Yao Z, Darowski K, St-Denis N, Wong V, Offensperger F, Villedieu A, Amin S, Malty R, Aoki H, Guo H, Xu Y, Iorio C, Kotlyar M, Emili A, Jurisica I, Babu M, Neel B, Gingras AC, and Stagljar I, A global analysis of the protein phosphatase interactome, Mol Cell, in press.
Petschnigg J, Kotlyar M, Blair L, Jurisica I, Stagljar I, and Ketteler R, Systematic identification of oncogenic EGFR interaction partners, J Mol Biol, in press.
Rahmati, S., Abovsky, M., Pastrello, C., Jurisica, I. pathDIP: An annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis. Nucl Acids Res, 45(D1): D419-D426, 2016.
Chehade, R., R. Pettapiece-Phillips, Salmena, L., Kotlyar, M., Jurisica, I., Narod, S. A., Akbari, M. R., Kotsopoulos, J. Reduced BRCA1 transcript levels in freshly isolated blood leukocytes from BRCA1 mutation carriers is mutation specific, Breast Cancer Res, 18(1): 87, 2016.
Cierna, Z., Mego, M., Jurisica, I., Machalekova, K., Chovanec, M., Miskovska, V., Svetlovska, D., Hainova, K., Kajo, K., Mardiak, J., Babal, P. Fibrillin-1 (FBN-1) a new marker of germ cell neoplasia in situ, BMC Cancer, 16: 597, 2016.

Thank you to members

This work would not be possible without the participation of World Community Grid Members. Thank you for generously contributing CPU cycles, and for your interest in this and other World Community Grid projects.

See the full article here.

Please help promote STEM in your local schools.

Stem Education Coalition

“World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
WCG projects run on BOINC software from UC Berkeley.

BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

“Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

Please visit the project pages-

FightAIDS@home Phase II

OpenZika

Help Stop TB

Outsmart Ebola together

Mapping Cancer Markers

Uncovering Genome Mysteries

Say No to Schistosoma

GO Fight Against Malaria

Drug Search for Leishmaniasis

Computing for Clean Water

The Clean Energy Project

Discovering Dengue Drugs – Together

Help Cure Muscular Dystrophy

Help Fight Childhood Cancer

Help Conquer Cancer

Human Proteome Folding

FightAIDS@Home

World Community Grid is a social initiative of IBM Corporation
IBM Corporation

IBM – Smarter Planet

From Nature: “[International] supercomputer, BOINC, needs more people power”

Nature

22 February 2017
Ivy Shih

Xinhua / Alamy Stock Photo

A citizen science initiative that encourages public donations of idle computer processing power to run complex calculations is struggling to increase participation.

Berkeley Open Infrastructure for Network Computing (BOINC), a large grid that harnesses volunteered power for scientific computing, has been running for 15 years to support research projects in medicine, mathematics, climate change, linguistics and astrophysics.

But, despite strong demand by scientists for supercomputers or computer networks that can rapidly analyse high volumes of data, the volunteer run BOINC has struggled to maintain and grow its network of users donating their spare computer power. Of its 4 million-plus registered users, only 6% are active, a number that has been falling since 2014.

“I’m constantly looking for ways to expose sectors of the general population to BOINC and it’s a struggle,” says David Anderson, a co-founder and computer scientist at the University of California Berkeley.

How many people use BOINC?

Many more people have registered with BOINC than actually donate their computer power (active users).
Anderson says BOINC, which is [no longer] funded by the National Science Foundation, currently hosts 56 scientific projects that span an international network of more than 760,000 computers. [current: 24-hour average: 17.367 PetaFLOPS. Active: 267,932 volunteers, 680,893 computers.]The platform’s combined processing power simulates a supercomputer whose performance is among the world’s top 10.

Access to such supercomputers can be expensive and require lengthy waits, so BOINC offers research groups access to processing power at a fraction of the prohibitive cost.

“A typical BOINC project uses a petaflop of computing — which typically costs maybe USD $100,000 a year. If you were to go to buy the same amount of computing power on the Amazon cloud, it would cost around $40 million,” says Anderson.

Kevin Vinsen, a scientist at the International Centre for Radio Astronomy Research, Australia, leads a project that analyses photos of galaxies. BOINC’s helps analyse the SkyNet’s huge dataset, which is especially valuable given the project’s shoestring budget.

“In BOINC I can have 20,000 people working on it at the same time. Each one is doing a small portion of the galaxy,” he says.

Anderson wants to connect BOINC to major supercomputer facilities in the United States, to reduce the lengthy wait researchers have to process their data. He is working to add the network to the Texas Advanced Computing Center as an additional resource for researchers.

Access to such supercomputers can be expensive and require lengthy waits, so BOINC offers research groups access to processing power at a fraction of the prohibitive cost.

“A typical BOINC project uses a petaflop of computing — which typically costs maybe USD $100,000 a year. If you were to go to buy the same amount of computing power on the Amazon cloud, it would cost around $40 million,” says Anderson.

Kevin Vinsen, a scientist at the International Centre for Radio Astronomy Research, Australia, leads a project that analyses photos of galaxies. BOINC’s helps analyse the SkyNet’s huge dataset, which is especially valuable given the project’s shoestring budget.

“In BOINC I can have 20,000 people working on it at the same time. Each one is doing a small portion of the galaxy,” he says.

Anderson wants to connect BOINC to major supercomputer facilities in the United States, to reduce the lengthy wait researchers have to process their data. He is working to add the network to the Texas Advanced Computing Center as an additional resource for researchers.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

Nature is a weekly international journal publishing the finest peer-reviewed research in all fields of science and technology on the basis of its originality, importance, interdisciplinary interest, timeliness, accessibility, elegance and surprising conclusions. Nature also provides rapid, authoritative, insightful and arresting news and interpretation of topical and coming trends affecting science, scientists and the wider public.

From WCG: “Community Achievements in 2016”

World Community Grid (WCG)

27 Dec 2016
Summary
We’re grateful for the volunteers and scientists who worked with us this year to launch two new research efforts, make progress on existing projects, and spread the word about volunteer computing to new audiences. Here are some of the highlights of 2016, which wouldn’t be possible without each of you.

Two new research projects, two awards, several conferences…and volunteers around the globe whose support made all of this progress possible. Because of you, 2016 was a great year for World Community Grid! Below are a few of this year’s highlights.

Helping Stop a Global Killer

Tuberculosis is one of the world’s deadliest disease, killing approximately 1.5 million people every year. In March, researchers at The University of Nottingham launched Help Stop TB on World Community Grid to study the molecular structure of the bacterium that causes tuberculosis, so that scientists can learn how to overcome it.

Thanks to votes from volunteers and supporters, an influential audience at South by Southwest (SXSW) learned how World Community Grid volunteers have supported humanitarian research projects since 2004, and heard how these volunteers helped scientists make a breakthrough that could bring clean water to millions. Listen to audio of our full presentation, which was given in March, or read about our experience.

Searching for Potential Treatments for Zika

The Zika virus began spreading rapidly through the Americas in 2015. In 2016, it continued moving north and was also reported in Asia. There is no effective treatment for Zika, no vaccine, and the virus as been linked to serious complications, including lifelong brain-related issues for infants whose mothers contract Zika while pregnant. In response to volunteer requests, we looked for a project to fight the virus, and in May, an international team of researchers launched the OpenZika project on World Community Grid to search through millions of chemical compounds for those that may become treatments.

Program manager Juan Hindo was invited to attend South by South Lawn 2016 at the White House in October. This first-time event brought together leaders in art, technology, innovation, and social change who are helping to improve the world. Read about Juan’s experience and how it inspired us to re-ssue our call for research projects that address climate change.

Winning Awards

We appreciate awards because they recognize and raise awareness for the important work made possible by World Community Grid volunteers.

Thanks to votes from volunteers and supporters, we were honored to receive a People’s Voice Webby Award in the Corporate and Social Responsiblity category. This award recognized our new online experience to help people learn about and join World Community Grid, which helped improve our sign-up rate. The Webby statuette traveled around the U.S. this summer and fall to spend time with each team member, as shown in the video below.

We also received a D&AD Wood Pencil Impact Award, which was created by the advertising industry to recognize programs that have a societal impact that helps change the status quo.

Thank You

Twelve years, 27 projects, and (as of November) 3 billion research results later, we are very grateful to the volunteers all over the world who are supporting basic science by donating unused computing time. Thanks for making 2016 a year of new beginnings and continued progress. Stay tuned for exciting news in early 2017!

See the full article here.

Please help promote STEM in your local schools.

Stem Education Coalition

“World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

WCG projects run on BOINC software from UC Berkeley.

BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

“Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

Please visit the project pages-

FightAIDS@home Phase II

OpenZika

Help Stop TB

Outsmart Ebola together

Mapping Cancer Markers

Uncovering Genome Mysteries

Say No to Schistosoma

GO Fight Against Malaria

Drug Search for Leishmaniasis

Computing for Clean Water

The Clean Energy Project

Discovering Dengue Drugs – Together

Help Cure Muscular Dystrophy

Help Fight Childhood Cancer

Help Conquer Cancer

Human Proteome Folding

FightAIDS@Home

World Community Grid is a social initiative of IBM Corporation
IBM Corporation

IBM – Smarter Planet