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  • richardmitnick 8:19 pm on May 16, 2017 Permalink | Reply
    Tags: , , , , WCG   

    From Help Fight Childhood Cancer at WCG: “Help Fight Childhood Cancer Project Researchers Publish a Paper” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    6 Jun 2016
    Represented 5.16.17

    Summary
    The Help Fight Childhood Cancer project searched for a cure for a particular childhood cancer. The researchers have found that some of the promising compounds they identified also show an antidepressant capability.

    Lay Summary:

    The Help Fight Childhood Cancer project researchers have published a paper on serendipitous results they found from the drug candidate search run on World Community Grid. The project originally searched for candidate compounds that targeted specific proteins to help cure a childhood brain cancer called neuroblastoma. Some of the targeted proteins are also involved in several psychological disorders. They have found that some of the identified compounds show an antidepressant capability. Furthermore, additional research might lead to potential treatments for Huntington’s disease and Alzheimer’s disease. The paper was published in the journal Neurochemistry International.

    Paper title: Effects of novel small compounds targeting TrkB on neuronal cell survival and depression-like behavior

    Authors: Mayu Fukuda, Atsushi Takotori, Yohko Nakamura, Akiko Suganami, Tyuji Hoshino, Yutaka Tamura, Akira Nakagawara

    Technical Abstract:

    Brain-derived neurotrophic factor (BDNF) and its high affinity receptor tyrosine kinase receptor B (TrkB) are involved in neuronal survival, maintenance, differentiation and synaptic plasticity. Deficiency of BDNF was reported to be associated with psychological disorders such as depression. Hence we examined proliferative effect of 11 candidate TrkB agonistic compounds in TrkB-expressing SH-SY5Y cells, via a hypothesis that some candidate compounds identified in our previous in silico screening for a small molecule targeting the BDNF binding domain of TrkB should activate TrkB signaling. In the present study, two promising compounds, 48 and 56, were identified and subsequently assessed for their ability to induce TrkB phosphorylation in vitro and in vivo. Likewise those seen in BDNF, the compounds mediated TrkB phosphorylation was blocked by the Trk inhibitor, K252a. Since BDNF-TrkB signaling deficiency is associated with the pathogenesis of depression and reactivation of this signaling by antidepressants is a cause of the pathogenic state recovery, the compounds were subjected to the assessment for forced swim test, which is a mouse model of depression. We found that compound 48 significantly reduced mouse immobility time compared with the control vehicle injection, suggesting the confirmation of hypothetical antidepressant-like efficacy of 48 compound in vivo. Thus, our present study demonstrated that compound 48, selected through in silico screening, is a novel activator of TrkB signaling and a potential antidepressant molecule.

    Click here to see the paper’s abstract online.

    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 Icon

    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.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “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

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    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

    faah-1-new-screen-saver

    faah-1-new

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

    IBM – Smarter Planet
    sp

     
  • richardmitnick 12:13 pm on May 15, 2017 Permalink | Reply
    Tags: , , , , WCG, You can Help Stamp Out EBOLA   

    From Nature: “Ebola vaccine could get first real-world test in emerging outbreak” 

    Nature Mag
    Nature

    12 May 2017
    Amy Maxmen

    The Democratic Republic of the Congo has reported nine suspected cases of infection in recent weeks.

    1
    The most recent Ebola epidemic, in West Africa from 2014 to 2016, killed more than 11,000 people. Jane Hahn/Washington Post

    An outbreak of the Ebola virus has emerged in the Democratic Republic of the Congo (DRC), the World Health Organization (WHO) said on 12 May.

    3
    Ebola virus virion. Created by GC microbiologist Cynthia Goldsmith, this colorized transmission electron micrograph (TEM) revealed some of the ultrastructural morphology displayed by an Ebola virus virion.
    Source Public Health Image Library, #10816

    Congolese authorities have reported nine suspected cases of Ebola infection in the past three weeks; the WHO has confirmed one, and tests are pending on others. Now health officials are considering whether to deploy an experimental Ebola vaccine against the outbreak, for the first time since the WHO gave it preliminary approval in April.

    The aid group Médecins Sans Frontières (MSF, also known as Doctors Without Borders) is discussing a potential vaccination campaign with the Congolese government, an MSF spokesperson says.

    2

    That would require the approval of the WHO, which has not decided whether to call on the approved experimental vaccine or others in development, says WHO spokesperson Tarik Jašarević. Still, he says, “we are taking this [outbreak] seriously because Ebola is always serious”. The most recent outbreak of the virus, in West Africa from 2014 to 2016, killed 11,325 people; there have been several known outbreaks in the DRC, but none has been as severe as the West African one.

    There are now 12 candidate Ebola vaccines in development. None is yet approved for sale, in part because the candidates were not ready for testing until the West African Ebola crisis was on the wane. But on 27 April, the WHO’s advisory group on immunization recommended that an experimental vaccine called rVSV-SEBOV be deployed promptly should an Ebola outbreak arise.

    Developed by the Public Health Agency of Canada and licensed by the drug companies NewLink Genetics of Ames, Iowa, and Merck of Kenilworth, New Jersey, rVSV-ZEBOV showed promise in a study published in The Lancet last December1. The trial included 11,841 people in Guinea in 2015, near the end of the Ebola outbreak there. None of the 5,837 people who received the vaccine had developed the disease ten days after vaccination. But there were 23 cases among the thousands of other people included in the trial.

    A look ahead

    The deployment of rVSV-ZEBOV may be warranted in the DRC, because the vaccine is based on the Zaire strain of Ebola — the same strain that is driving the current outbreak, says Anthony Fauci, director of the US National Institute of Allergy and Infectious Diseases. If public-health authorities decide to proceed, there is a supply of rVSV-ZEBPV at the ready: Gavi, the Vaccine Alliance, signed an agreement with Merck in 2016 to purchase 300,000 doses of vaccine for use in future outbreaks.

    Historically, outbreaks in the DRC have never approached the unprecedented severity of the West Africa epidemic. The most recent Ebola outbreak in the DRC occurred in the Bas-Uele province — the site of the current episode — and killed 49 people over 3 months. The gap in severity is due in part to the DRC’s infrastructure and geography. Whereas people, and the viruses they carry, travel fluidly between Guinea, Sierra Leone and Liberia, rough roads impede movement in many parts of the DRC. This means that outbreaks there kill people, but fizzle out without spreading very far.

    The DRC also benefits from Ebola expertise that its doctors and researchers have built up over the years. Jean-Jacques Muyembe-Tamfum, director-general of the National Institute for Biomedical Research in Kinshasa, is well known among Ebola experts for curbing the DRC’s first outbreak, in 1976, and many thereafter. He works to engage affected communities immediately, to build their trust in medical teams and to help them understand the importance of not touching others in checking the spread of the virus.

    Muyembe-Tamfum “is probably out there already”, says David Heymann, an infectious-disease epidemiologist at the London School of Hygiene and Tropical Medicine. He recalls how Muyembe-Tamfum — who could not be reached for comment — helped to contain past outbreaks by telling village chiefs that Ebola was an evil spirit, which passes to people when they touch the infected. “Muyembe talks with people in a way that they will understand quickly,” Heymann says. “He does whatever he believes is effective, and it is.”

    References
    See the full article for references with links.

    See the full article here .

    You can Help Stamp Out EBOLA.

    This WCG project runs at Scripps Institute

    Scripps

    Outsmart Ebola Together

    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.

    MyBOINC

    Please help promote STEM in your local schools.

    STEM Icon

    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.

     
  • richardmitnick 1:52 pm on May 12, 2017 Permalink | Reply
    Tags: , , , WCG   

    From WCG: Ebola outbreak 

    New WCG Logo

    WCGLarge

    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.

    2
    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 Icon

    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.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “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

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    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

    faah-1-new-screen-saver

    faah-1-new

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

    IBM – Smarter Planet
    sp

     
  • richardmitnick 3:37 pm on April 28, 2017 Permalink | Reply
    Tags: , , sciencestarter.com, WCG   

    From sciencestarter.com blog via WCG: “Help accelerate biomedical research from the comfort of your couch” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    1

    sciencestarter.com blog

    April 27th, 2017
    Jenny Cutraro

    1
    No scalpel required!
    Learn how to identify images of clogged blood vessels to accelerate Alzheimer’s research or trace 3D images of neurons to shed light on how these structures influence behavior.
    SciStarter’s editors hand-picked five, biomedical research projects we think you’ll love. You can do these free projects and contribute to research all from the comfort of home!
    Find more projects and events on SciStarter, to do now or bookmark for later.
    Bonus: Complete your SciStarter profile this month and we’ll send you a free digital copy of The Rightful Place of Science: Citizen Science.
    Cheers!
    The SciStarter Team

    2
    EyesOnALZ
    Speed up Alzheimer’s research simply by clicking on video images that show clogged (or “stalled”) blood vessels. Scientists think stalled blood flow may contribute to Alzheimer’s and they need your help to identify stalls in short videos of (real!) ultrasound images. All ages are welcome to participate. You’ll view a brief tutorial before you get started.
    Location: Online
    Get started!

    3
    The Biomedical Citizen Science Hub (CitSciBio)
    Find and share biomedical citizen science resources through the National Institute of Health-supported CitSciBio. This hub is your source for resources, projects, references, methods and communities about biomedical citizen science research.
    Location: Online
    Get started!

    4
    Mozak: Brainbuilder
    Humans still outperform computers at identifying complex shapes like neurons. Simply trace 3D images of brain neurons (on your computer) to shed light on how neuron structure influences brain function. Since Mozak launched in November, citizen scientists (like you!) have reconstructed neurons 3.6 times faster than earlier methods!
    Location: Online
    Get started!

    5
    Mark2Cure If you can read, you can help. With Mark2Cure you are trained to identify scientific concepts and mark, or annotate, those concepts in scientific literature. Help scientists find information they need to solve complex problems.
    Location: Online
    Get started!

    6
    Citizen Endo
    Help improve the medical field’s understanding of endometriosis symptoms on daily life. You can participate (with or without endometriosis) by tracking your daily experiences using the Phendo app.
    Location: Online
    Get started!

    7

    Find an event on SciStarter

    Crowd and Cloud is now streaming online. This four-part public television series explores citizen science, crowdsourcing, and mobile technology.
    Watch now

    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 Icon

    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.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “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

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    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

    faah-1-new-screen-saver

    faah-1-new

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

    IBM – Smarter Planet
    sp

     
  • richardmitnick 12:13 pm on April 27, 2017 Permalink | Reply
    Tags: , , , Crédit Agricole contributes computer power to WCG, WCG   

    From WCG: ““It’s not just big data. It’s for the good of humanity.” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    27 Apr 2017

    Summary
    Three co-workers wanted their company to support World Community Grid, but they knew they’d need to convince many people to make their vision a reality. Here’s how they did it.

    Each year, employees with SILCA (one of the information technology and services arms of Crédit Agricole, an international bank based in France) are invited to submit proposals for new company initiatives at Crédit Agricole’s Innovation Week. In 2015, a small group at SILCA presented a carefully crafted proposal to run World Community Grid on company computers. Their proposal led to a successful pilot project, and eventually a wide-scale implementation that currently includes more than 1,200 computers.

    1
    David Dubuis, Philippe Mangematin, and Stephane Douglay at Innovation Week 2017, after their successful pilot of World Community Grid won an Innovation Award. (Photo by Alain Goulard)

    A Carefully Planned Pilot

    Social responsibility, environmental responsibility, and solidarity are very strong values within SILCA. So when David Dubius, Philippe Mangematin, and Stephane Douglay learned about World Community Grid several years ago, they realized that this was an opportunity for their organization to donate unused computing power from its desktops for important humanitarian research.

    “First, we planned a pilot project that involved 10 computers,” explains David. “We presented a proposal for this pilot project to a jury at Innovation Week 2015, and it was considered one of the best proposals of the year.”

    As the IT department for a bank, SILCA is strongly committed to security at every level. To pre-emptively address security questions about World Community Grid, the pilot project team created a proof of concept plan. Their pilot project included communicating frequently with World Community Grid’s development team, and discussing any new security questions as they came up.

    The team also showed their colleagues at SILCA how much they could potentially contribute to research projects to combat AIDS, Ebola, Zika, cancer, and other diseases. “We monitored the data flow daily, and turned in weekly reports that detailed exactly what the computers in the pilot project were doing,” says David. They also enlisted the help of Dr. Alessandra Carbone, who led the Help Cure Muscular Dystrophy project. Dr. Carbone, who is based in France, worked with the team to create a podcast where she explained how useful and important World Community Grid was for her research, and for humanitarian science projects in general.

    An Award and an Expansion

    By January 2017, the team was ready to showcase the results of the pilot project at another Innovation Week. With their presentation “Desktop Grid, Soyons Solidaires,” they received a first-prize Innovation Award out of 60 projects presented within the Crédit Agricole group. Their message, “It’s not just big data, it’s for the good of humanity,” had once again resonated with the Innovation Week judges.

    SILCA formalized its collaboration with World Community Grid in December 2016, becoming an official partner and installing the World Community Grid app on 1,200 workstations of its employees.

    Plans for the Future

    The team is working on internal marketing efforts to continue to spread the word within SILCA, such as working with their communications team to put a World Community Grid widget on SILCA’s intranet site.

    The team would like to extend the project to other groups within Crédit Agricole. “SILCA is just one subsidiary of Crédit Agricole,” says David. “We are presenting the results of our project to other groups, and it would be a great victory if others would join.”

    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 Icon

    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.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “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

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    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

    faah-1-new-screen-saver

    faah-1-new

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

    IBM – Smarter Planet
    sp

     
  • richardmitnick 3:24 pm on April 24, 2017 Permalink | Reply
    Tags: Move to IBM Cloud, WCG   

    From WCG: “World Community Grid Moves to IBM Cloud” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    24 Apr 2017

    Summary
    On May 15, World Community Grid will begin migrating to IBM Cloud, as part of an effort to modernize and enhance our infrastructure capabilities. Our system will be unavailable for approximately 48 hours while the migration takes place, but otherwise the move will not affect most volunteers.

    1
    We’re happy to announce that World Community Grid is moving to IBM Cloud. Through this migration, we are leveraging more scalable and powerful hosting capabilities, as well as IBM and open source automation tools that make our development and deployment processes more efficient. This allows us to identify, diagnose and address major technical issues more quickly. Most significantly, IBM Cloud’s global footprint of more than 50 data centers across 19 countries allows us to expand more easily and prepares us for years of growth.

    The migration will begin on May 15 and is expected to last approximately 48 hours, during which World Community Grid will be unavailable. This means that volunteers will not be able to access the website, fetch new research or return completed work during that time.

    No action is required by most volunteers, as our systems will resume sending and receiving research tasks once the migration is complete. However, for individuals or organizations who have restricted firewall rules, you may need to update those rules in order to continue contributing, by allowing connections to our new IP address (169.47.63.74).

    Anyone with questions about this migration can post in this forum thread. We appreciate everyone’s support during this migration, which will provide a modern hosting environment for volunteers and researchers for years to come.

    See the full article here.

    Please help promote STEM in your local schools.
    STEM Icon

    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.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    MyBOINC

    “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

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    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

    faah-1-new-screen-saver

    faah-1-new

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

    IBM – Smarter Planet
    sp

     
  • richardmitnick 1:48 pm on April 10, 2017 Permalink | Reply
    Tags: , , , WCG   

    From OpenZika at WCG: “OpenZika Researchers Continue Calculations and Prepare for Next Stage” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    By: The OpenZika research team
    21 Mar 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 status of their calculations and their continuing work to spread the word about the project.

    Zika depiction. Image copyright John Liebler, www.ArtoftheCell.com

    Project Background

    While the Zika virus may not be getting the continuous press coverage that it received in 2015 and 2016, it is still a threat to the health of people across the globe. New infections continue to be reported in both South America and North America, and medical workers are just beginning to assess the effects of the virus on young children whose mothers were infected while pregnant.

    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 US Food and Drug Administration (FDA) agency, but few to none of the “hit” compounds that have been identified thus far are both potent enough against Zika virus and also safe for pregnant women.

    Also, there are a number of efforts underway to develop a vaccine against the Zika virus. However, vaccines do not help people who already have the infection. It will be several years before they are proven effective and safe, and before enough doses can be mass produced and distributed. And even after approved vaccines are available and distributed to the public, not all people will be vaccinated. Consequently, in the meantime and in the future, cures for Zika infections are needed.

    ZIKV NS3 helicase bound to RNA with the predicted binding modes of five approved drugs (from our second set of candidates) selected by virtual screening. These candidates are shown as surfaces with different shades of green. The identification of these candidates and the video were made by Dr. Alexander L. Perryman [see below].

    We began the analysis phase of the project by focusing on the results against the apo NS3 helicase crystal structure (apo means that the protein was not bound to anything else, such as a cofactor, inhibitor, or nucleic acid) to select our first set of candidates, which are currently being assayed by our collaborator at University of California San Diego, Dr. Jair L. Siqueira-Neto, using cell-based assays. The NS3 helicase is a component of the Zika virus that is required for it to replicate itself.

    In the second set of screening results that we recently examined, we used the new crystal structure of NS3 helicase bound to RNA as the target (see the images / animation above). Similar to the first set of candidates, we docked approximately 7,600 compounds in a composite library composed of the US Food and Drug Administration-approved drugs, the drugs approved in the European Union, and the US National Institutes of Health clinical collection library against the new RNA-bound structure of the helicase. Below are the results of this second screening:

    232 compounds passed the larger collection of different energetic and interaction-based docking filters, and their predicted binding modes were inspected and measured in detail.
    Of the compounds that were inspected in detail, 19 unique compounds passed this visual inspection stage of their docked modes.
    From the compounds that passed the visual inspection, 9 passed subsequent medicinal chemistry-based inspection and will be ordered soon.

    Status of the calculations

    In total, we have submitted 2.56 billion docking jobs, which involved the virtual screening of 6 million compounds versus 427 different target sites. We have already received approximately 1.9 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 different docking jobs need to be returned to World Community Grid, re-organized, and then compressed before sending them to our server.)

    Except for a few stragglers, we have received all of the results for our experiments that involve docking 6 million compounds versus the proteins 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 against the NS2B / NS3 protease.

    A new stage of the project

    We just finished preparing and testing the docking input files that will be used for the second stage of this project. Instead of docking 6 million compounds, we will soon be able to start screening 30.2 million compounds against these 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, many 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, called AutoDock Vina, could properly use each pdbqt file 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), 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 six months this massive new library of compounds is 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!!!

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

    Our PLoS Neglected Tropical Diseases paper, OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery, was published on October 20, and it has already been viewed over 4,000 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 accepted by F1000Research and viewed > 3800 times.

    A group from Brazil, coordinated by Prof. Glaucius Oliva, has 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 the NS5 protein of Zika virus. They have solved two high-resolution crystal structures of ZIKV NS5, which have been recently released on the PDB (Protein Data Bank) (PDB ID: 5TIT and 5U04).

    Our paper entitled “Molecular Dynamics simulations of Zika Virus NS3 helicase: Insights into RNA binding site activity” was just accepted for publication 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 already performed against NS3 helicase, and the molecular dynamics simulations generated new conformations of this protein that we will use as input targets in new virtual screens that we perform as part of OpenZika.

    Additional News

    We have applied and been accepted to present OpenZika: Opening the Discovery of New Antiviral candidates against Zika Virus and Insights into Dynamic behavior of NS3 Helicase to the 46th World Chemistry Congress. The conference will be held in Sao Paulo, Brazil, on July 7-14.

    Dr. Sean Ekins has hired a postdoc and a master 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 offered to buy 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.


    Dr. Alex Perryman models an OpenZika shirt. Profits from the sale of OpenZika merchandise go to purchasing compounds for lab testing. (Photo by Keith Bratcher, courtesy of Rutgers University)

    Alexander L. Perryman, Ph.D., is a senior researcher (Research Teaching Specialist III) in the lab, with extensive training in computational methods in drug discovery and in the biochemical mechanisms of multi-drug-resistance in infectious diseases. He is a member of the Center for Emerging & Re-emerging Pathogens, in the Department of Pharmacology, Physiology & Neuroscience. Alex started performing research in Professor Cleo Samudzi’s X-ray crystallography lab as a freshman in the undergraduate Biochemistry program at the University of Missouri-Columbia (“Mizzou” or MU). He then became a Beckman Scholar in Professor Thomas P. Quinn’s protein structure & radiopharmaceuticals lab at MU. He received his Ph.D. in Biomedical Sciences from the University of California, San Diego (UCSD) School of Medicine (Pharmacology Department) as a Howards Hughes Medical Institute fellow in H.H.M.I. Principal Investigator J. Andrew McCammon’s lab. As a graduate student, Alex used Molecular Dynamics simulations to (a) predict a mechanism of multi-drug-resistance for “super bug” mutants of HIV protease, (b) to predict the existence of allosteric binding sites on the surface of HIV protease and then (c) to test the utility of exploiting that allosteric relationship. These predictions are now supported by an ever-growing body of experimental evidence. He also helped create the “Relaxed Complex Scheme,” which was one of the first methods to incorporate the flexibility of the target protein into docking studies of potential drug-like compounds. He conducted post-doctoral research at the California Institute of Technology (“Caltech”) as an Amgen fellow in the Division of Biology. He then became a Research Associate in Prof. Arthur J. Olson’s lab at The Scripps Research Institute (TSRI), where he ran the day-to-day operations of the FightAIDS@Home project (the largest computational drug discovery project devoted to HIV/AIDS, which runs on IBM’s World Community Grid). He also designed, led, and ran the day-to-day operations for the largest computational drug discovery project ever performed against malaria, the GO Fight Against Malaria project, also on IBM’s World Community Grid. GO FAM involved screening 5.6 million compounds against 22 different classes of drug targets (including targets from Mycobacterium tuberculosis, as well). GO Fight Against Malaria was the first academic project to ever perform over 1 billion different docking jobs. His experience is highlighted by over 24 publications and one US patent.

    In the Freundlich lab, Alex has broadened his experience by becoming an expert at developing and applying machine learning models and other ligand-based techniques to advance Mtb research, as well as projects against the ESKAPE pathogens. He has also created several machine learning models to help address key shortcomings in chemical tool discovery and drug development (such as metabolic stability, cytotoxicity, and solubility). For a change, Dr. Perryman has also been getting his hands wet–purifying proteins and performing enzyme inhibition assays, to help test his new computational predictions against Mtb targets.

    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 Icon

    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.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    MyBOINC

    “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

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    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

    faah-1-new-screen-saver

    faah-1-new

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

    IBM – Smarter Planet
    sp

     
  • richardmitnick 2:03 pm on April 6, 2017 Permalink | Reply
    Tags: , , , WCG   

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

    New WCG Logo

    WCGLarge

    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.

    1
    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.

    2
    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.

    3
    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.

    4
    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 Icon

    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.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    MyBOINC

    “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

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    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

    faah-1-new-screen-saver

    faah-1-new

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

    IBM – Smarter Planet
    sp

     
  • richardmitnick 2:34 pm on March 28, 2017 Permalink | Reply
    Tags: , , WCG   

    Clean Energy from WCG: “Clean Energy Project Researchers Sharing Results and Planning for the Future” 

    WCG
    World Community Grid

    Clean Energy

    Clean Energy Project

    By: The Clean Energy Project team
    Harvard University
    28 Mar 2017

    Summary
    The Clean Energy Project team is working on publicizing their results to-date. They have wrapped up the second phase of the project, and are also making decisions about their future work with World Community Grid.

    Remember this video from a couple of years ago about the goals of the Clean Energy Project? Thanks to the many volunteers who supported this study, the researchers were able to collect an enormous amount of data, which they are now analyzing and getting ready to publish.


    The Clean Energy Project research team at Harvard would like to thank the volunteers who supported us through two phases of the project! Currently, we are getting ready to share our findings in at least one publication and a conference. We are also weighing different options for further work with World Community Grid, which might include new types of calculations on solar cells or perhaps a study with a much larger scope.

    Publishing Our Results

    We have completed our screening of non-fullerene acceptor materials for new organic photovoltaic devices. The findings were quite interesting and have kept us very busy! We describe our results in a manuscript that was submitted to the high-impact journal Energy & Environmental Science.

    Steven Lopez will travel to San Francisco to present this work at the American Chemical Society national meeting in April 2017. Alán has presented the results of the Clean Energy Project in several forums and they have helped inform the screening for other materials, such as organic flow batteries, in his research group.

    Considering our findings, we are working hard to continue developing what we have learned with this initial study. Our work may have led to the discovery of a new class of non-fullerene acceptors, with excellent properties including low production costs! We will reveal the chemical identities of these exciting derivatives when the paper is published.

    How Scientific Papers Get Published

    The process of peer-review scientific publishing is not so straightforward and can take many months, or even years in some cases.

    First, the manuscript of a paper is sent to an editor, which decides whether the work will be reviewed at all. Depending on the journal, this can be just one out of every five manuscripts received. Then, three to five experts in the field independently assess the manuscripts that are accepted for review. Each reviewer must certify that the researchers’ approach and results are novel and worth publishing.

    If the panel decides that a manuscript should be published, they will put forth suggestions and concerns that the manuscript’s authors respond to. Typically, after these concerns and edits have been addressed, the publishing agency will recommend that a paper be published. If it is to be published online, it usually become available in 1-2 weeks.

    Future Work with World Community Grid

    We have not been able to submit work units for volunteer calculation because we had been working to expand the number of molecules we will test by using a low-cost computational method to evaluate the properties of potential photovoltaic materials. With our efficient calibration scheme, this would allow us to screen 10-100 times as many candidates in the same amount of time. If this process can be fully optimized, we could begin generating these work units for volunteers. Benjamin Sanchez-Lengeling has pushed this aspect of the project forward; keep an eye on this rising star!

    However, it is also possible that we may go in a different direction altogether. Another idea we are considering is to use these efficient computational methods to catalog the properties of molecules that benefit humanity and have applications beyond clean energy. Molecular Space is vast and full of useful molecules for the world.

    We appreciate everyone’s patience while we take stock of the resources and personnel available in our lab, and make decisions about the best scientific use of the generous donations of computing time provided by World Community Grid volunteers.

    Thanks again to everyone for your support of this project over the years,

    Alán Aspuru-Guzik and Steven Lopez
    On Behalf of the CEP Team

    See the full article here.

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The Harvard Clean Energy Project Database contains data and analyses on 2.3 million candidate compounds for organic photovoltaics. It is an open resource designed to give researchers in the field of organic electronics access to promising leads for new material developments.

    Would you like to help find new compounds for organic solar cells? By participating in the Harvard Clean Energy Project you can donate idle computer time on your PC for the discovery and design of new materials. Visit WorldCommunityGrid to get the BOINC software on which the project runs.

    CleanEnergyProjectPartners

    CEP runs on software from BOINC, Berkeley Open Infrastructure for Network computing.

    BOINCLarge

     
  • richardmitnick 1:48 pm on March 24, 2017 Permalink | Reply
    Tags: , , WCG   

    From Help Stop TB at WCG: “Help Stop TB Team Selects Data Analysis Tools” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    By: The Help Stop TB Team
    University of Nottingham
    28 Feb 2017

    Summary
    The Help Stop TB team is hard at work analyzing the data they’ve received so far from World Community Grid. They recently chose two new data analysis tools, which will help them better understand the behavior of the bacterium which causes tuberculosis.

    Hello everyone, and thank you for contributing your computer time to Help Stop TB! We would have never completed so many simulations if it wasn’t for you!

    Background

    Help Stop TB was created to examine a particular aspect of the highly resistant and adaptable bacterium that causes tuberculosis. The bacterium has an unusual coat which protects it from many drugs and the patient’s immune system. Among the fats, sugars and proteins in this coat, the TB bacterium contains a type of fatty molecules called mycolic acids. Our project simulates the behavior of these molecules in their many configurations to better understand how they offer protection to the TB bacteria. With the resulting information, scientists may be able to design better ways to attack this protective layer and therefore develop better treatments for this deadly disease.

    Choosing Data Analysis Tools and Methods

    Since our previous mini update in November, Athina has been focusing on analysing our simulation data, and at the same time she is writing up her PhD thesis. As a team, we have now achieved our main goal, which was to come up with a robust and efficient analytical strategy. This will enable us to efficiently process the heaps of data we’re receiving from the simulations conducted by World Community Grid volunteers, and will answer our questions about mycolic acids’ conformational behaviour and its biological implications.

    The analysis protocol that we have decided on combines a variety of different analytical tools and methods. One of the tools we are using is a PCA (principal components analysis) clustering technique developed at the School of Pharmacy at the University of Nottingham. This tool has helped us categorise the shapes that mycolic acids adopt throughout the simulations. In turn, this gives us a clearer idea about which shapes are the most dominant ones.

    Figures 1 and 2 below are examples of how we are looking at the shapes of mycolic acids. These structures are important as we are looking at all the possible conformations that mycolic acids can assume in order to try to understand how those molecules work, how their conformations dictate any biological implications and/or affect the disease itself, in the hope to find any links and discover more for prevention methods.

    Because it has been shown that mycolic acids tend to demonstrate complex conformational behaviours with frequent folding and unfolding events, it is important to assess the frequency of those events. Understanding the frequency in which mycolic acids change from one folding conformation into another may help underpin important aspects of their biological behaviour.

    1
    Figure 1. Summary of a mycolic acid predominant clusters and their respective representative structures. This figure outlines the clusters’ transitions and dependency as well as their relative percentages.

    Additionally, the length of time that the molecules choose to remain in a certain adopted conformational pattern may also elucidate further biological implications. Each molecule assumes different shapes throughout its folding pathway and these shapes can be very dependent to each other. From the PCA clustering tool data, we have extracted important information regarding the dependency (Figure 1) between the different shapes the molecules assume.

    Another analytical approach that we employed was the distance matrix analysis. We created and analysed matrices (Figure 2) of the distances of all the carbon atoms along the mycolic acid chain. This method can provide further insight into the frequency of the folding events and can also help us understand more about the flexibility of each structure.

    2
    Figure 2. Distance matrices of two very different conformations of a mycolic acid. These matrices show the distances of carbon atoms along the mycolic acid chain in these two conformations, and provide a good visual idea of how different the various folding patterns are.

    We have also tested the suitability of a dihedral angle clustering tool which was developed at the Centre for Molecular Design (CMD) at the University of Portsmouth. This tool was computationally less intensive than the distance matrix analysis, but unfortunately it could not address the frequent refolding events that the mycolic acids demonstrate, thus making it challenging to extract meaningful data. However, the test cases that we analysed with this technique confirmed the predominant clusters that we had found with our PCA tools. We will now use the best choice of analysis options to build a picture for all the different mycolic acids, and will subsequently link the individual behaviour with experimental data on mycolic acid population in bacterial cell walls and their individual roles therein.

    That was all our news for now! Thank you again for your contributions, and let’s all wish good luck to Athina with her writing! Until the next time, happy crunching!

    See the full article here.

    Please help promote STEM in your local schools.
    STEM Icon

    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.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    MyBOINC

    “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

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    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

    faah-1-new-screen-saver

    faah-1-new

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

    IBM – Smarter Planet
    sp

     
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