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  • richardmitnick 1:49 pm on August 8, 2018 Permalink | Reply
    Tags: , , , Maping Cancer Markets project takes on sarcoma, , WCG-World Community Grid   

    From World Community Grid (WCG): “Sarcoma Dataset Coming Soon to Mapping Cancer Markers Project” 

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    From World Community Grid (WCG)

    8 Aug 2018
    Dr. Igor Jurisica

    In this comprehensive update, the Mapping Cancer Markers team explains how they are determining which genes and gene signatures carry the greatest promise for lung cancer diagnosis. They also introduce the next type of cancer–sarcoma–to be added soon to the project.

    The Mapping Cancer Markers (MCM) project continues to process work units for the ovarian cancer dataset. As we accumulate these outcomes, we continue to analyze MCM results from the lung cancer dataset. In this update, we discuss preliminary findings from this analysis. In addition, we introduce the sarcoma dataset that will be our focus in the next stage.

    Patterns of gene-family biomarkers in lung cancer

    In cancer, and human biology in general, multiple groups of biomarkers (genes, protein, microRNAs, etc.) can have similar patterns of activity and thus clinical utility, helping diagnosis, prognosis or predicting treatment outcome. For each cancer subtype, one could find large number of such groups of biomarkers, each having similar predictive power; yet current statistical and AI-based methods identify only one from a given data set.

    We have two primary goals in MCM: 1) to find good groups of biomarkers for the cancers we study, and 2) to identify how and why these biomarkers form useful groups, so we can build a heuristic approach that will find such groups for any disease without needing months of computation on World Community Grid. The first goal will give us not only information that after validation may be useful in clinical practice, but importantly, it will generate data that we will use to validate our heuristics.

    1
    Illustration 1: Proteins group by similar interactions and similar biological functions.

    Multiple groups of biomarkers exist primarily due to the redundancy and complex wiring of the biological system. For example, the highly interconnected human protein-protein interaction network enables us to see how individual proteins perform diverse molecular functions and together contribute to a specific biological process, as shown above in Illustration 1. Many of these interactions change between healthy and disease states, which in turn affects the functions these proteins carry. Through these analyses, we aim to build models of these processes that in turn could be used to design new therapeutic approaches.

    Two specific groups of biomarkers may appear different from each other, yet perform equivalently because the proteins perform similar molecular functions. However, using these groups of biomarkers for patient stratification may not be straightforward. Groups of biomarkers often do not validate in new patient cohorts or when measured by different biological assays, and there are thousands of possible combinations to consider. Some groups of biomarkers may have all reagents available while others may need to be develop (or be more expensive); they may also have different robustness, sensitivity and accuracy, affecting their potential as clinically useful biomarkers.

    At the present time, there is no effective approach to find all good groups of biomarkers necessary to achieve the defined goal, such as accurately predicting patient risk or response to treatment.

    The first goal of the Mapping Cancer Markers project is to gain a deeper understanding of the “rules” of why and how proteins interact and can be combined to form a group of biomarkers, which is essential to understanding their role and applicability. Therefore, we are using the unique computational resource of World Community Grid to systematically survey the landscape of useful groups of biomarkers for multiple cancers and purposes (diagnosis and prognosis). Thereby, we established a benchmark for cancer gene biomarker identification and validation. Simultaneously, we are applying unsupervised learning methods such as hierarchical clustering to proteins that group by predictive power and biological function.

    The combination of this clustering and the World Community Grid patterns enables us to identify generalized gene clusters that provide deeper insights to the molecular background of cancers, and give rise to more reliable groups of gene biomarkers for cancer detection and prognosis.

    Currently, we are focusing on the first-phase results from the lung cancer dataset, which focused on a systematic exploration of the entire space of potential fixed-length groups of biomarkers.

    3
    Illustration 2: Workflow of the MCM-gene-pattern-family search. The results of the World Community Grid analysis combined with the unsupervised clustering of genes identifies a set of gene-pattern-families, generalizing the groups of biomarkers. Finally, the results are evaluated using known cancer biomarkers and by using functional annotations, such as signaling pathways, gene ontology function and processes.

    As depicted above in Illustration 2, World Community Grid computed about 10 billion randomly selected groups of biomarkers, to help us understand the distribution of which group sizes and biomarker combinations perform well, which in turn we will use to validate heuristic approaches. Analysis showed that about 45 million groups of biomarkers had a high predictive power and passed the quality threshold. This evaluation gives us a detailed and systematic picture of which genes and gene groups carry the most valuable information for lung cancer diagnosis. Adding pathway and protein interaction network data enables us to further interpret and fathom how and why these groups of biomarkers perform well, and what processes and functions these proteins carry.

    Simultaneously, we used the described lung cancer data to discover groups of similar genes. We assume that these genes or the encoded proteins fulfill similar biological functions or are involved in the same molecular processes.

    3
    Illustration 3: Evaluation of the hierarchical clustering of the lung cancer data, using the complete linkage parameter, for different numbers of groups indicated by the K-values (100 to 1000). The first plot shows the silhouette value – a quality metric in this clustering, i.e., measure of how well each object relates to its cluster compared to other clusters. The second plot depicts the inter- and intra-cluster distance and the ratio of intra/inter cluster distance.

    To find the appropriate clustering algorithms and the right number of gene groups (clusters) we use different measures to evaluate the quality of each of the individual clustering. For instance, Illustration 3 (above) shows the results of the evaluation of the hierarchical clustering for different numbers of clusters. To evaluate clustering quality, we used silhouette value (method for assessing consistency within clusters of data, i.e., measure of how well each object relates to its own cluster compared to other clusters). A high silhouette value indicates good clustering configuration, and the figure shows a large increase in the silhouette value at 700 gene groups. Since this indicates a significant increase in quality, we subsequently select this clustering for further analysis.

    Not all combinations of biological functions or the lack of it will lead to cancer development and will be biologically important. In the next step, we apply a statistical search to investigate which combinations of clusters are most common among the well-preforming biomarkers, and therefore result in gene groups or pattern families. Since some gene-pattern-families are likely to occur even at random, we use enrichment analysis to ensure the selection only contains families that occur significantly more often than random.

    In the subsequent step we validated the selected generalized gene-pattern-families using an independent set of 28 lung cancer data sets. Each of these studies report one or several groups of biomarkers of up- or down-regulated genes that are indicative for lung cancer.


    Illustration 4: Shown is a selection of high performing pattern families and how they are supported by 28 previously published gene signatures. Each circle in the figure indicates the strength of the support: The size of the circle represents the number of clusters in the family that where found significantly more often in the signature of this study. The color of the circle indicates the average significance calculated for all clusters in the pattern-family.

    5
    Illustration 5: One of the most frequent gene-pattern-families, is a combination of cluster 1, 7 and 21. We annotated each cluster with pathways using pathDIP and visualized it using word clouds (the larger the word/phrase, the most frequently it occurs).

    The word cloud visualization indicates that cluster 7 is involved in pathways related to GPCRs (G protein–coupled receptor) and NHRs (nuclear hormone receptors). In contrast, the genes in cluster 1 are highly enriched in EGFR1 (epidermal growth factor receptor) as well as translational regulation pathways. Mutations affecting the expression of EGFR1, a transmembrane protein, have shown to result in different types of cancer, and in particular lung cancer (as we have shown earlier, e.g., (Petschnigg et al., J Mol Biol 2017; Petschnigg et al., Nat Methods 2014)). The aberrations increase the kinase activity of EGFR1, leading to hyperactivation of downstream pro-survival signaling pathways and a subsequent uncontrolled cell division. The discovery of EGFR1 initiated the development of therapeutic approaches against various cancer types including lung cancer. The third group of genes are common targets of microRNAs. Cluster 21 indicates strong involvement with microRNAs, as we and others have shown before (Tokar et al., Oncotarget 2018; Becker-Santos et al., J Pathology, 2016; Cinegaglia et al., Oncotarget 2016).

    6
    Illustration 6: Evaluation of enriched pathways for cluster 1. Here we used our publicly available pathway enrichment analysis portal pathDIP (Rahmati et al., NAR 2017). The network was generated with our network visualization and analysis tool NAViGaTOR 3 (http://ophid.utoronto.ca/navigator).

    The final illustration evaluates the 20 most significantly enriched pathways for cluster 1. The size of the pathway nodes corresponds to the number of involved genes, and the width of the edges corresponds the number genes of overlapping between pathways. One can see that all pathways involved in translation are highly overlapping. mRNA-related pathways form another highly connected component in the graph. The EGFR1 pathway is strongly overlapping with many of the other pathways, indicating that genes that are affected by those pathways are involved in a similar molecular mechanism.

    Sarcoma

    After lung and ovarian cancers, next we will focus on sarcoma. Sarcomas are a heterogeneous group of malignant tumors that are relatively rare. They are typically categorized according to the morphology and type of connective tissues that they arise in, including fat, muscle, blood vessels, deep skin tissues, nerves, bones and cartilage, which comprises less than 10% of all malignancies (Jain 2010). Sarcomas can occur anywhere in the human body, from head to foot, can develop in patients of any age including children, and often vary in aggressiveness, even within the same organ or tissue subtype (Honore 2015). This suggests that a histological description by organ and tissue type is neither sufficient for categorization of the disease nor does it help in selecting the most optimal treatment.

    Diagnosing sarcomas poses a particular dilemma, not only due to their rarity, but also due to their diversity, with more than 70 histological subtypes, and our insufficient understanding of the molecular characteristics of these subtypes (Jain 2010).

    Therefore, recent research studies focused on molecular classifications of sarcomas based on genetic alterations, such as fusion genes or oncogenic mutations. While research achieved major developments in local control/limb salvage, the survival rate for “high-risk” soft tissue sarcomas (STSs) has not improved significantly, especially in patients with a large, deep, high-grade sarcoma (stage III) (Kane III 2018).

    For these reasons, in the next phase of World Community Grid analysis, we will focus on the evaluation of the genomic background of sarcoma. We will utilize different sequencing information and technologies to gain a broader knowledge between the different levels of genetic aberrations and the regulational implications. We will provide a more detailed description of the data and the incentives in the next update.

    Petschnigg J, Kotlyar M, Blair L, Jurisica I, Stagljar I, and Ketteler R, Systematic identification of oncogenic EGFR interaction partners, J Mol Biol, 429(2): 280-294, 2017.
    Petschnigg, J., Groisman, B., Kotlyar, M., Taipale, M., Zheng, Y., Kurat, C., Sayad, A., Sierra, J., Mattiazzi Usaj, M., Snider, J., Nachman, A., Krykbaeva, I., Tsao, M.S., Moffat, J., Pawson, T., Lindquist, S., Jurisica, I., Stagljar, I. Mammalian Membrane Two-Hybrid assay (MaMTH): a novel split-ubiquitin two-hybrid tool for functional investigation of signaling pathways in human cells; Nat Methods, 11(5):585-92, 2014.
    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, 2017.
    Kane, John M., et al. “Correlation of High-Risk Soft Tissue Sarcoma Biomarker Expression Patterns with Outcome following Neoadjuvant Chemoradiation.” Sarcoma 2018 (2018).
    Jain, Shilpa, et al. “Molecular classification of soft tissue sarcomas and its clinical applications.” International journal of clinical and experimental pathology 3.4 (2010): 416.
    Honore, C., et al. “Soft tissue sarcoma in France in 2015: epidemiology, classification and organization of clinical care.” Journal of visceral surgery 152.4 (2015): 223-230.
    Tokar T, Pastrello C, Ramnarine VR, Zhu CQ, Craddock KJ, Pikor L, Vucic EA, Vary S, Shepherd FA, Tsao MS, Lam WL, Jurisica Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes. Oncotarget. 9(10):9137-9155, 2018
    Becker-Santos, D.D., Thu, K.L, English, J.C., Pikor, L.A., Chari, R., Lonergan, K.M., Martinez, V.D., Zhang, M., Vucic, E.A., Luk, M.T.Y., Carraro, A., Korbelik, J., Piga, D., Lhomme, N.M., Tsay, M.J., Yee, J., MacAulay, C.E., Lockwood, W.W., Robinson, W.P., Jurisica, I., Lam, W.L., Developmental transcription factor NFIB is a putative target of oncofetal miRNAs and is associated with tumour aggressiveness in lung adenocarcinoma, J Pathology, 240(2):161-72, 2016.
    Cinegaglia, N.C., Andrade, S.C.S., Tokar, T., Pinheiro, M., Severino, F. E., Oliveira, R. A., Hasimoto, E. N., Cataneo, D. C., Cataneo, A.J.M., Defaveri, J., Souza, C.P., Marques, M.M.C, Carvalho, R. F., Coutinho, L.L., Gross, J.L., Rogatto, S.R., Lam, W.L., Jurisica, I., Reis, P.P. Integrative transcriptome analysis identifies deregulated microRNA-transcription factor networks in lung, adenocarcinoma, Oncotarget, 7(20): 28920-34, 2016.

    Other news

    We have secured a major funding from Ontario Government for our research: The Next Generation Signalling Biology Platform. The main goal of the project is developing novel integrated analytical platform and workflow for precision medicine. This project will create an internationally accessible resource that unifies different types of biological data, including personal health information—unlocking its full potential and making it more usable for research across the health continuum: from genes and proteins to pathways, drugs and humans.

    We have also published papers describing several tools, portals and applications with our collaborators. Below we list those most related directly or indirectly to work on World Community Grid:

    Wong, S., Pastrello, C., Kotlyar, M., Faloutsos, C., Jurisica, I. SDREGION: Fast spotting of changing communities in biological networks. ACM KDD Proceedings, 2018. In press. BMC Cancer, 18(1):408, 2018.
    Kotlyar, M., Pastrello, C., Rossos, A., Jurisica, I. Protein-protein interaction databases. Eds. Cannataro, M. et al. Encyclopedia of Bioinformatics and Computational Biology, 81, Elsevier. In press. doi.org/10.1016/B978-0-12-811414-8.20495-1
    Rahmati, S., Pastrello, C., Rossos, A., Jurisica, I. Two Decades of Biological Pathway Databases: Results and Challenges, Eds. Cannataro, M. et al. Encyclopedia of Bioinformatics and Computational Biology, 81, Elsevier. In press.
    Hauschild, AC, Pastrello, C., Rossos, A., Jurisica, I. Visualization of Biomedical Networks, Eds. Cannataro, M. et al. Encyclopedia of Bioinformatics and Computational Biology, 81, Elsevier. In press.
    Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, Ceol A, Cesareni G, Combe C, De Las Rivas J, Del-Toro N, Heimbach J, Hermjakob H, Jurisica I, Koch M, Licata L, Lovering RC, Lynn DJ, Meldal BHM, Micklem G, Panni S, Porras P, Ricard-Blum S, Roechert B, Salwinski L, Shrivastava A, Sullivan J, Thierry-Mieg N, Yehudi Y, Van Roey K, Orchard S. Encompassing new use cases – level 3.0 of the HUPO-PSI format for molecular interactions. BMC Bioinformatics, 19(1):134, 2018.
    Minatel BC, Martinez VD, Ng KW, Sage AP, Tokar T, Marshall EA, Anderson C, Enfield KSS, Stewart GL, Reis PP, Jurisica I, Lam WL., Large-scale discovery of previously undetected microRNAs specific to human liver. Hum Genomics, 12(1):16, 2018.
    Tokar T, Pastrello C, Ramnarine VR, Zhu CQ, Craddock KJ, Pikor L, Vucic EA, Vary S, Shepherd FA, Tsao MS, Lam WL, Jurisica, I. Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes. Oncotarget. 9(10):9137-9155, 2018.
    Paulitti A, Corallo D, Andreuzzi E, Bizzotto D, Marastoni S, Pellicani R, Tarticchio G, Pastrello C, Jurisica I, Ligresti G, Bucciotti F, Doliana R, Colladel R, Braghetta P, Di Silvestre A, Bressan G, Colombatti A, Bonaldo P, Mongiat M. Matricellular EMILIN2 protein ablation ca 1 uses defective vascularization due to impaired EGFR-dependent IL-8 production, Oncogene, Feb 27. doi: 10.1038/s41388-017-0107-x. [Epub ahead of print] 2018.
    Tokar, T., Pastrello, C., Rossos, A., Abovsky, M., Hauschild, A.C., Tsay, M., Lu, R., Jurisica. I. mirDIP 4.1 – Integrative database of human microRNA target predictions, Nucl Acids Res, D1(46): D360-D370, 2018.
    Kotlyar M., Pastrello, C., Rossos, A., Jurisica, I., Prediction of protein-protein interactions, Current Protocols in Bioinf, 60, 8.2.1–8.2.14., 2017.
    Singh, M., Venugopal, C., Tokar, T., Brown, K.B., McFarlane, N., Bakhshinyan, D., Vijayakumar, T., Manoranjan, B., Mahendram, S., Vora, P., Qazi, M., Dhillon, M., Tong, A., Durrer, K., Murty, N., Hallet, R., Hassell, J.A., Kaplan, D., Jurisica, I., Cutz, J-C., Moffat, J., Singh, D.K., RNAi screen identifies essential regulators of human brain metastasis initiating cells, Acta Neuropathologica, 134(6):923-940, 2017.

    Thank you.

    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.


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    Please help promote STEM in your local schools.

    Stem Education Coalition

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

    Microbiome Immunity Project

    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

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    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
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  • richardmitnick 9:29 am on July 4, 2018 Permalink | Reply
    Tags: , Carbon nanostructures, , WCG-World Community Grid   

    From World Community Grid (WCG): “The Expanding Frontiers of Carbon Nanotube Technology” 

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    From World Community Grid (WCG)

    3 Jul 2018

    Summary
    The Clean Water Project made an exciting discovery about the possible applications of carbon nanostructures to water purification, biomedical research, and energy research. Dr. Ming Ma, one of the scientists on the project, recently published a paper that summarizes the current status of work in this field.

    1
    The team at Tsinghua University includes (left to right) Ming Ma, Kunqi Wang, Wei Cao, and Jin Wang. Not pictured: Yao Cheng

    Dr. Ming Ma (of the Computing for Clean Water project) at Tsinghua University recently published a paper in the Journal of Micromechanics and Microengineering entitled “Carbon nanostructure based mechano-nanofluidics.” The paper is a thorough survey of all the recent research work on fluid flow in carbon nanostructures, such as carbon nanotubes and graphene sheets.

    Carbon atoms can form single-atom thick sheets known as graphene. When these are rolled into tube shape, they are called carbon nanotubes. In recent years, there has been a flurry of research work with these nanostructures, called that because they deal with very tiny atomic structures measured in nanometers (billionths of a meter). The Computing for Clean Water project is one example of recent research in this area: By using World Community Grid to simulate water flow through carbon nanotubes at an unprecedented level of detail, the project’s research team discovered that under specific conditions, certain kinds of natural vibrations of atoms inside the nanotubes can lead to a 300% increased rate of diffusion (a kind of flow) of water through the nanotubes.

    Among their many surprising properties are the ability to dramatically enhance water flow through or past the nanostructures. There is much research being conducted to understand how this happens and ultimately how to make best use of this property to potentially purify water, desalinate water, and meet other goals in biomedical and energy research. Challenges remain in how to efficiently manufacture these materials and how to adjust their structures to achieve the best results.

    Thanks to everyone who supported this project.

    See the full article here.


    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

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

    Microbiome Immunity Project

    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
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  • richardmitnick 3:07 pm on June 27, 2018 Permalink | Reply
    Tags: , Help Cure Muscular Dystrophy project, WCG-World Community Grid   

    From World Community Grid (WCG): “Data from Help Cure Muscular Dystrophy Project Helps Shed Light on the Mysteries of Protein Interactions” 

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    From World Community Grid (WCG)

    26 Jun 2018
    Dr. Alessandra Carbone
    Sorbonne Université

    Summary
    Protein-protein interactions are the basis of cellular structure and function, and understanding these interactions is key to understanding cell life itself. Dr. Alessandra Carbone and her team continue to analyze data on these interactions from the Help Cure Muscular Dystrophy project, and they recently published a new paper to contribute to the body of knowledge in this field.


    29 mminutes

    Dr. Alessandra Carbone (principal investigator of the Help Cure Muscular Dystrophy project) and team have published a paper entitled “Hidden partners: Using cross-docking calculations to predict binding sites for proteins with multiple interactions” in the journal Proteins.

    Protein interactions are the basis for most biological functions. How they interact with each other and other compounds (such as DNA, RNA, and ligands) in the cell is key to understanding life and disease functions. Complicating things, proteins often interact with more than one other kind of protein. To better understand protein functions, tools are required to uncover these potential interactions.

    Different parts (surfaces) of the protein can be binding sites that attract another protein. This paper describes a methodology the research team developed to better predict these alternative binding sites. A subset of the Help Cure Muscular Dystrophy project data was used to validate their technique, which will be subsequently applied to the whole dataset computed via World Community Grid.

    See the full article here.


    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

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

    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-

    Microbiome Immunity Project

    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 8:43 am on May 23, 2018 Permalink | Reply
    Tags: , , , , WCG-World Community Grid   

    From World Community Grid (WCG): “FightAIDS@Home – Phase 2 Prepares for A New Stage” 

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    World Community Grid (WCG)

    By: The FightAIDS@Home research team
    22 May 2018

    Summary
    The FightAIDS@Home – Phase 2 researchers are making plans to write a paper and to test new compounds as part of the continuing search for new and better treatments.

    1
    No image caption or credit.

    Background

    Researchers all over the world have been making advances in the battle against HIV/AIDS for many years. However, AIDS-related complications still affect far too many people. UNAIDS estimates that 36.7 million people were living with HIV in 2016. And while AIDS-related deaths have decreased significantly since their peak in 2005, approximately 1 million people died of causes related to AIDS in 2016. (See the UNAIDS website for more statistics.)

    HIV continues to be a challenge because it quickly mutates in ways that make existing drug treatments ineffective. FightAIDS@Home joined World Community Grid more than a decade ago with the simple but challenging goal of finding new treatments for HIV. During Phase 1 of the project, the team identified thousands of potentially promising candidates to be confirmed experimentally in the lab. However, because it’s cost and time prohibitive to lab test all the potential candidates, Phase 2 was created to prioritize the candidate compounds by evaluating them with more accurate methods.

    Current Work

    Our team is processing the current type of work units through World Community Grid as quickly as possible. Once these work units are completed, we plan to write a paper about the process, including its strengths, limitations, and lessons learned.

    We are also planning to use World Community Grid’s computing power to analyze new compounds that are important to our work with the HIVE Center at the Scripps Research Institute. This work will begin after we run a sample of these new compounds on our own grid computing network.

    Thank You

    We appreciate everyone who continues to donate their computing power to the search for better anti-HIV treatments. We also encourage everyone to opt in to Phase 2 of the project—the more quickly we can run through the current work units, the sooner we can move ahead to new compounds.

    See the full article here.

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


    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.
    stem
    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 1:53 pm on April 29, 2018 Permalink | Reply
    Tags: , Impact of atmospheric aerosols on climate change (Far Eastern Federal University- Russia), Impact of climate change on public health (Emory University USA), Rainfall modeling in Africa (Delft University of Technology- Netherlands), WCG-World Community Grid   

    From World Community Grid (WCG): “Announcing Three Winning Climate Change Projects” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    Announcing Three Winning Climate Change Projects

    26 Apr 2018

    Summary
    After a rigorous review of dozens of applications from all over the world, we’re excited to announce the research groups who will receive supercomputing power, weather data, and cloud storage from IBM to accelerate climate change science.

    1

    As our planet faces the mounting impacts of climate change, scientists are on the front lines of understanding complex consequences and developing solutions.

    We’ve heard from climate change scientists that common bottlenecks they face include limited access to weather data, and insufficient computing power and data storage capacity to accurately simulate the impacts of climate change.

    These are some of the reasons why IBM Corporate Citizenship recently invited scientists to apply for grants of massive computing power from World Community Grid, meteorological data from The Weather Company, and data storage from IBM Cloud Object Storage to support their climate change or environmental research projects. (More information about these IBM resources can be found here.)

    As our planet faces the mounting impacts of climate change, scientists are on the front lines of understanding complex consequences and developing solutions. Common bottlenecks facing scientists conducting foundational research include limited access to weather data, and insufficient computing power and data storage capacity to accurately simulate the impacts of climate change.

    To build on IBM’s decades-long commitment to environmental stewardship, IBM Corporate Citizenship is helping overcome these roadblocks by donating technology and data to three foundational climate change research projects.

    Groundbreaking Research Projects

    These IBM resources–crowdsourced computing power through World Community Grid, weather data from The Weather Company, and IBM Cloud Object Storage–will support three groundbreaking new research projects, chosen from over 70 applications for their potential to make a significant contribution to our understanding of climate change impacts and potential solutions.

    Impact of climate change on public health (Emory University, USA)

    This project will examine the impact of climate change on temperature and air pollution at local levels, helping researchers understand the impact of a changing climate on human health.

    Impact of atmospheric aerosols on climate change (Far Eastern Federal University, Russia)

    Atmospheric aerosols, such as dust, smoke and pollution, both absorb and reflect sunlight in the atmosphere, and represent the greatest area of uncertainty in climate science today, according to the UN Intergovernmental Panel on Climate Change (IPCC). This project aims to determine how super-micron particles (6 to 12 micrometers in diameter) interact with sunlight and how they contribute to atmospheric temperatures – information that will improve the accuracy of climate models.

    Rainfall modeling in Africa (Delft University of Technology, Netherlands)

    In Africa, agriculture relies heavily on localized rainfall, which is difficult to predict. In collaboration with the Trans-African Hydro-Meteorological Observatory, researchers will simulate rainfall on the continent – information that could help farmers be more resilient, among other weather and hydrology applications.

    In return for this support, the winning scientists agree to publicly release the data from their collaboration with IBM, enabling the global community to benefit from and build upon their findings.

    Supercharged by IBM Resources

    Each of these three winning projects will use one or more of these resources:
    Crowdsourced computing power

    Scientists receive free, 24/7 access to computing power through World Community Grid, a philanthropic initiative of IBM that enables anyone with a computer or Android device to support scientific research by carrying out virtual research experiments on their devices.

    Through the contributions of over 740,000 individuals and 440 organizations, the initiative has enabled a number of breakthrough discoveries in environmental research by helping scientists discover new materials for efficient solar energy, study the impact of management policies on large watershed areas and uncover more efficient ways to filter water.

    “World Community Grid enabled us to find
    new possibilities for solar cells on a
    timescale that matters to humanity–in other
    words, in a few years instead of decades.”

    Dr. Alan Aspuru-Guzik
    Professor of Chemistry and Chemical Biology
    Harvard University

    Weather data

    The historical and real-time weather data of The Weather Company, an IBM business, can help scientists advance our understanding of environmental systems and support the design of solutions to prevent, mitigate against, and adapt to climate change.

    Cloud storage

    For scientists who work on environmental research initiatives with very large data sets, IBM Cloud Object Storage provides a scalable platform to store and analyze the results of virtual experiments on World Community Grid and conduct further investigations.
    Frequently Asked Questions
    What is World Community Grid?
    We’re a philanthropic initiative of IBM that connects researchers with free and massive computing power, donated by volunteers around the world, to advance scientific research on our planet’s most pressing issues. Anyone with a computer or Android device can sign up to participate. To date, over 740,000 individuals and 430 organizations have contributed over a billion years of computing power to support 29 research projects, including studies about low-cost water filtration systems and new materials for capturing solar energy efficiently.

    Our research partners have published over 50 peer-reviewed scientific papers in journals including Science, Nature and PLOS. This crowdsourced computing power, which is provided to researchers for free, often allows them to take on research efforts at an unprecedented scale, pursue new research approaches and get the work done in years instead of decades.

    How does World Community Grid work?
    Scientists from institutions all over the world come to us with research projects that need massive amounts of computing power. Using their research simulation or modeling software tool of choice, we integrate that software into our platform and distribute millions of virtual research experiments to thousands of World Community Grid volunteers, who perform these calculations on their computers and Android devices. World Community Grid validates and bundles the results of these calculations and sends them back to the researchers. Through World Community Grid, scientists can not only access massive computing power at no cost, but can also engage the public in their research.

    What climate and environmental research has World Community Grid supported to date?

    Since 2004, World Community Grid has supported a number of environmental research efforts including:

    Clean Energy Project – In what is believed to be the largest quantum chemistry experiment ever performed, researchers at Harvard University screened millions of organic photovoltaic compounds to predict their potential for converting sunlight into electricity. Amongst these, 36,000 were predicted to double the efficiency of most carbon-based solar cells currently in production.
    Computing for Clean Water – Researchers at Tsinghua University in Beijing used World Community Grid to simulate the flow of water through carbon nanotubes at an unprecedented level of detail. In doing so, they discovered a phenomenon that points to a new possibility for water filtration which could one day improve access to clean water for the nearly one billion people around the world who lack access to it.

    Computing for Sustainable Water – Scientists at University of Virginia studied the impact of management policies on water quality in the Chesapeake Bay to gain deeper insights into what actions can lead to restoration, health and sustainability of this important water resource.
    Uncovering Genome Mysteries – Researchers examined 200 million genes from a wide variety of life forms, such as microorganisms found on seaweed from Australian coastlines and in the Amazon river. The goal of their work is to augment knowledge about biochemical processes in general, identify how organisms interact with each other and the environment, and document the current baseline microbial diversity, allowing a better understanding of how microorganisms change under environmental stresses, such as climate change.

    What kind of computing power is being made available with the grant?

    Scientists who receive these awards will use World Community Grid, a philanthropic IBM initiative that provides scientists with massive amounts of computing power, for free. Through World Community Grid, computational research calculations are distributed to thousands of volunteers around the world who perform these calculations on their computer or Android devices.

    In addition, we carry out the technical work to integrate the researchers’ computational research tool of choice into the World Community Grid platform. We also provide communications and outreach support to engage and educate the public in this research.

    How is the computing power being made available by World Community Grid different from a supercomputer?
    As one of the researchers who has used World Community Grid for several years once said, “It turns out that having hundreds of thousands of computers in parallel accelerates things more than having a supercomputer.” World Community Grid provides scientists with 24/7 access to enough computing power to match some of the world’s most powerful supercomputers. But unlike a traditional supercomputer, World Community Grid distributes the computational work to thousands of computers worldwide, each of which is provided by a volunteer who chooses to make their device available to conduct scientific calculations. For our research partners, this means not having to wait in line for computing resources as they would with most supercomputers at their own institutions. Instead, they receive free access to massive amounts of computing power, while engaging the public in their research.

    What weather data is being made available to grant recipients?
    Grant recipients have free access to weather data from The Weather Company, an IBM business, to support their research. The data may include global weather forecasts, historical observations, and current weather conditions. Access to the data will be provided through web-based APIs, while the project runs on World Community Grid.

    What cloud storage capabilities are being made available to grantees?
    Grant recipients have free access to IBM Cloud Object Storage for all data storage needs related to their IBM-supported project, while the project runs on World Community Grid. Technical assistance will also be provided to assess their data storage needs and determine appropriate storage solutions.

    What were the criteria for successful proposals?
    Successful proposals met the following criteria:

    Not for profit: conducted by public or nonprofit organizations
    Tackle climate change: Advance understanding of the impacts of climate change, and/or strategies to adapt to or mitigate the impacts of climate change.
    Contribute to open science: all data generated by World Community Grid volunteers must be made freely available to the scientific community.
    Enabled, accelerated or enhanced by the resources we offer: climate or environmental computational studies that require significant computer processing power and can be divided into small independent computations, may need weather data, and/or could benefit from large amounts of cloud-based storage.

    How were applications evaluated?
    A team of IBM scientists and outside scientists with expertise in environmental and climate change science reviewed each application for:

    Scientific merit
    Potential to contribute to the global community’s understanding of specific climate change and/or environmental science challenges
    Capacity of the research team to manage a sustained research project
    Demonstrated need for IBM resources

    What commitment do scientists make in return?
    In return for these free resources, scientists agree to support our open data policy by publicly releasing the research data from their World Community Grid project, to enable the global scientific community to benefit from and build upon their findings. Research teams also agree to engage the volunteers in their research through regular communications through World Community Grid communication channels.

    When will these projects begin running on World Community Grid?
    We have begun the onboarding process for the projects, and are planning to launch the first project later in 2018. We will be posting updates about this process on our website.

    Can researchers still apply for these resources?
    We’re not currently accepting applications that include data from The Weather Company and storage from IBM Cloud, but any researchers who are interested in using World Community Grid’s computing power are welcome to submit an application.

    How do I make sure that I start contributing to these projects as soon as they’re launched?

    If you are already a World Community Grid volunteer, go to the My Projects page, where you can choose to opt in to new projects as they become available.

    If you’re not yet a World Community Grid volunteer, you can sign up to be notified as soon as the first of these three projects is launched. You can also join World Community Grid right now and support our existing projects.

    NOTIFY ME OF PROJECT LAUNCHES

    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 9:48 am on April 21, 2018 Permalink | Reply
    Tags: , , , WCG-World Community Grid, What's tech got to do with it?   

    From World Community Grid (WCG): “What’s tech got to do with it?” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    We went to SXSW to talk about how volunteer computing can help save the planet.

    20 Apr 2018
    Summary
    World Community was invited to give two presentations on the power of crowdsourced computing power at SXSW 2018 in Austin, Texas. See the full presentations, as well as a short video with excerpts from both, in this article.

    We were thrilled to be invited to give two presentations in the Code and Programming track at SXSW 2018. You can see both presentations in full, as well as a few excerpts in the first video below.

    In this short video, two scientists talk about the crucial issues they’re researching: climate change and clean energy. World Community Grid project manager Juan Hindo and software developer Jonathan Armstrong explain the important role of volunteers in accelerating research.

    Last year, IBM issued a call for proposals to climate change and environmental researchers, offering them not only World Community Grid supercomputing power, but also data from The Weather Company and storage on IBM Cloud Object Storage. In this video, IBM Distinguished Engineer and Chief Scientist Lloyd Treinish joins Juan and Jonathan to talk about the most pressing issues in climate change, the extent of the climate change science community’s technical needs, and the opportunity for the tech community to help.

    Dr. Alan Aspuru-Guzik was the lead researcher for the Clean Energy Project, which uncovered a large number of potential new and improved solar cells. In this presentation, Alan gave an overview of the work so far, and talked about his plans for further extending his collaboration with World Community Grid and other organizations.

    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 Cancer4

    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 5:01 pm on February 20, 2018 Permalink | Reply
    Tags: , , WCG-World Community Grid   

    From WCG: “The Whats and Whys of Basic Research” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    31 Oct 2017

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

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

    Vannevar Bush,
    “Science, the Endless Frontier”

    1
    Dr. Akira Nakagawara (pictured at right in his lab) has led two research projects that used World Community Grid to find new and better treatments for childhood cancer. The first project not only found seven drug compounds that could fight childhood cancer, but also discovered that two of these compounds might help treat depression.

    What is basic research?

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

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

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

    In another example, the researchers working on the Computing for Clean Water project wanted to study how to filter water more efficiently. This applied research led to some basic research findings which discovered some new properties about how water molecules interact with the walls of carbon nanotubes. These properties might prove useful in future applied research to develop better ways of removing salt from water and even some medical applications.


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

    Why is it crucial for continued scientific discovery?

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

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

    Why is public involvement in this type of research so important?
    “Basic research is often misunderstood, because it often seems to have no immediate payoff.”

    Massachusetts Institute of Technology,
    “The Future Postponed”

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

    If you recognize the importance of basic research and its place in science, you’re better equipped to support the scientific fields and projects that are most important to you. In addition to joining World Community Grid to donate your unused computing time to humanitarian research projects, you can join scientific organizations in your local community, and find and support additional citizen science projects in a wide variety of areas. Just as every computer is important to World Community Grid projects, every effort you make to support science makes a difference.

    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 Cancer4

    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 12:33 pm on February 17, 2018 Permalink | Reply
    Tags: , Uncovering Genome Mysteries Project, 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 [In social media just now]

    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.

    Background

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

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

    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-
    Smash Childhood Cancer4

    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 9:35 pm on December 1, 2017 Permalink | Reply
    Tags: , , , , , WCG-World Community Grid   

    From Mapping Cancer Markers at WCG: “New Facility and Expanded Plans for the Mapping Cancer Markers Research Team” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    30 Nov 2017
    Dr. Igor Jurisica
    Krembil Research Institute, University Health Network, Toronto

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

    1
    The Mapping Cancer Markers project is currently processing data to identify biomarkers for ovarian cancer, one of the deadliest cancers for women.

    After more than 17 years at Ontario Cancer Institute (now Princess Margaret Cancer Centre), we got an opportunity to join Krembil Research Institute (KRI) to work on a more complex approach to chronic diseases, where we moved in mid-November. KRI is still part of the University Health Network in Toronto, but focuses also on arthritis, neuroscience, and vision. The research and translational clinical research interests focus not only on diagnosis and improved treatment, but importantly on prevention, which aligns with my group’s interest over the last few years.

    Thus, MCM has not been negatively affected—the physical move was smooth, and our severs stayed in the original server rooms, reducing the risk of any hiccup for World Community Grid work units and results. We will not only continue, but will expand on our research.

    New Computational Biology Platform

    Importantly, we are in the finalizing stages of paperwork to embark on a newly-funded research by the Ontario Government: The Next Generation Signalling Biology Platform. This will provide us funds to create a software infrastructure for the comprehensive, integrative computational biology analyses workflows, in collaboration with translational research and clinical trials groups. Our partners are Princess Margaret Cancer Centre, Krembil Research Institute, University of Toronto, University of Montreal, BC Cancer Agency, Cancer Clinical Trials Group, Queen’s University, and European Bioinformatics Institute (IMEx Consortium). Besides focusing on cancer, this is our first large osteo-arthritis research project.

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

    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 Cancer4

    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 7:49 pm on November 24, 2017 Permalink | Reply
    Tags: , , , The BOINC Workshop 2017, WCG-World Community Grid   

    From WCG: “Plans for Future Development Discussed at BOINC Workshop 2017” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    22 Sep 2017 [Just appeared in RSS]
    Summary
    A group of BOINC developers, project managers, researchers, and volunteers recently participated in a workshop where they exchanged information and ideas that will help set the direction for the future development of the BOINC open source project.

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

    1
    World Community Grid’s Keith Uplinger (left) and Kevin Reed (right) were able to see a few of the iconic sights of Paris when they attended the BOINC Workshop 2017.

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

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

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

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

    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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