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  • richardmitnick 7:34 pm on November 24, 2017 Permalink | Reply
    Tags: , , , WCG-World Community Grid   

    From Uncovering Genome Mysteries Project at WCG: “Analysis Underway on 30 Terabytes of Data” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    24 Nov 2017

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


    In this video, Dr. Torsten Thomas explains the primary goals of the Uncovering Genome Mysteries project.

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

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

    Transferring 30 Terabytes of Data

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

    Data Processing and Analysis at Fiocruz

    The Fiocruz team has been busy with the further processing of the primary output of the project. In the workflow, raw data are expanded and deciphered, associated with the correct inter-genome comparisons, checked for errors, tabulated, and associated with many different data objects to transform that into meaningful information.

    The team is dealing with the rapidly growing size of the database, and purchased and installed new hardware (600 Tb) to help accommodate all the data. They also wish to build a database interface that appeals to the general public interested in biodiversity, and not only to scientists who specialize in functional analysis of encoded proteins in genomes of particular life forms.

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

    Searching for Partnerships

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

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

    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 2:39 pm on September 26, 2017 Permalink | Reply
    Tags: , , , , Smash Childhood Cancer, WCG-World Community Grid   

    From WCG: “The Road Ahead for Help Fight Childhood Cancer” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    26 Sep 2017
    Dr. Akira Nakagawara, MD, PhD
    CEO of the Saga Medical Center KOSEIKAN and President Emeritus, Chiba Cancer Center

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

    1
    No image caption or credit.

    Background

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

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

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

    Current Research

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

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

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

    4
    Smash Childhood Cancer

    Regarding the development of ALK inhibitors (see article https://www.ncbi.nlm.nih.gov/pubmed/15972965), candidate compounds as inhibitors were found in the in-silico screening, and analysis on cultured cancer cells was completed. Because of the lack of research personnel, unfortunately preclinical tests have not yet progressed.

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

    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-

    Smash Childhood Cancer
    4

    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 4:20 pm on July 17, 2017 Permalink | Reply
    Tags: , Ethical Corporation, , , WCG-World Community Grid   

    From WCG via Ethical Corporation: “How IBM is using the world’s surplus computer power to help the planet” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    1

    Ethical Corporation

    Jul 14, 2017
    Jennifer Ryan Crozier

    IBM’s Jennifer Ryan Crozier on how the open-source World Community Grid is advancing climate solutions by allowing researchers to complete thousands of years’ worth of research in just a few years

    2
    No image caption or credit.

    Summer heat used to mean summer fun. But this year, the first days of summer were ushered in by an ominous new study published in Nature Climate Change by Dr.Camilo Mora of the University of Hawaii. Mora and his team of researchers are predicting that without major reductions in greenhouse gases, up to 75% of the world’s population will be in danger of dying from heat by the year 2100. According to The Weather Company, an IBM business, “Global surface temperature has increased by around 1.8°F (1.0°C) since the late 1800s. More than half of this increase has occurred since the 1970s, and every decade since then has been warmer than the one before it.”

    The growing impact of climate change – including more drought, water shortages, intense storms, rising sea levels, and extremely hot weather – has galvanized scientists around the world to work overtime in the search for solutions, often with limited resources. Their work will figure prominently in making the Paris Agreement real, which was forged in 2015 as a pledge by countries worldwide to combat climate change with lower carbon emissions.

    Recently business, academic and science communities with a presence in the US loudly reiterated their strong support for the accord, joining collaborative action such as the We Are Still In coalition.

    Over the last few decades, the private sector has discovered the innovation related to sustainability is not only the right thing to do, but is also good for business. Customers want to do business with environmentally responsible businesses, and companies reap efficiencies that make them more competitive and creative. In fact, IBM itself has saved an enormous amount of money and done its part for the environment by meeting its own emissions and renewable energy sourcing commitments years ahead of schedule.

    But we want to do more. We want to equip the science community with the kind of resources it needs to fight climate change. Computational research is one such powerful tool for advancing climate change research and developing solutions. In fact, in awarding the 2013 Nobel Prize in Chemistry to a group of computer scientists who pioneered the field, the Prize Committee remarked that: “Today the computer is just as important a tool as the test tube.” The rapid growth in big data also holds valuable new insights. But to uncover those insights and leverage these techniques, scientists need much more computing power than they typically have access to. 

    World Community Grid addresses that gap. IBM’s World Community Grid is a crowd-sourced virtual supercomputer that is powered by the surplus computing power of computers and Androids donated by individual volunteers and organizations. Instead of wasting energy when idle or not in full use, hundreds of thousands of these devices redirect otherwise unused processing power to research scientists to collectively perform virtual experiments at an unprecedented scale.

    Through the contributions of over 730,000 volunteers and 430 organizations, worth $400m, World Community Grid’s research partners have completed the equivalent of thousands of years of work in just a few years, enabling important advances in environmental science.

    For example, scientists at Harvard University used World Community Grid to run the Clean Energy Project, the world’s largest quantum chemistry experiment with the goal of identifying new materials for solar energy. In just a few years, they analyzed millions of chemical compounds to predict their efficiency at converting sunlight into electricity. Their discovery of thousands of promising compounds will advance the development of cheap, flexible solar cell materials that we hope will be used worldwide to reduce carbon emissions and contribute to the fight against climate change.

    3

    Another project, designed by a team of international researchers and led by scientists at Tsinghua University in China [Computing for Clean Water], undertook an unprecedented, massive computational simulation study powered by IBM’s World Community Grid. They found that the use of carbon nanotubes, under specific conditions, could potentially lead to more efficient water filtering with less expense and less impact on the environment. Another World Community Grid project helped scientists study the impact of water management and development policies on large watershed areas.


    WCG Computing for Clean Water Project

    World Community Grid has also enabled medical breakthroughs. For instance, the Chiba Institute in Japan identified seven novel drug candidates that could potentially be used in new medicines that fight childhood neuroblastoma, one of the most common and dangerous childhood cancers. Tests showed that even at remarkably low doses, these drug candidates are very effective at killing cancer cells with no immediately apparent side effects.

    WCG Fighting Childhood Cancer

    This week, the scientific community is being offered a new opportunity to advance the quest for ways to combat climate change. IBM is inviting scientists around the world to apply for a technology grant (valued at $40m) of crowd-sourced supercomputing power, meteorological data from The Weather Company, and IBM Cloud storage to support their climate or environmental research project.

    Up to five of the most promising environmental and climate-related research projects will be supported, with technology and services contributions valued commercially at approximately $200 million.

    These resources can support many potential areas of inquiry, such as impacts on fresh water resources, predicting migration patterns, and developing models to improve crop resilience.

    Proposals will be evaluated for scientific merit, potential to contribute to the global community’s understanding of specific climate and environmental challenges and development of effective strategies to mitigate them, and the capacity of the research team to manage a sustained research project. 

    In return for this support, winning scientists agree to support open science by publicly releasing the research data from their collaboration with us, enabling the global community to benefit from and build upon their findings. 

    Scientists from around the world are encouraged to apply at https://www.worldcommunitygrid.org/climate.action, with a first round deadline of 15 September. Individuals and organisations can also support this work by joining http://www.worldcommunitygrid.org to donate their spare computing power to the winning research projects. 

    Climate change is a serious threat to people and our planet. And time is of the essence. We know that businesses and citizens themselves are critical to meet this challenge. IBM is proud to stand with the #WeAreStillIn coalition, the broadest cross section of the American economy that has pledged its commitment to help continue leading the global fight against climate change. All of us must be a part of the solution. World Community Grid is giving scientists, citizens and their computers the ability to work around the clock for change. 

    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

     
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