||Total Run Time (y:d:h:m:s)
|OpenPandemics – COVID-19
- project website
- Scripps youtube channel
COVID-19 is a disease caused by SARS-CoV2, a virus of the coronavirus family. These viruses cause diseases that affect mainly the human respiratory system and potentially other major organs. COVID-19 can lead to serious illness or even death.
As of the launch of this project, there is no treatment, cure, or vaccine for COVID-19.
Scientists at Scripps Research are doing molecular modeling simulations to look for possible candidates for the development of treatments for COVID-19, but to be successful they need massive computing power to carry out millions of simulated laboratory experiments.
So Scripps Research is partnering with World Community Grid, an IBM social impact initiative that allows anyone with a computer and an internet connection to donate their device’s computing power to help scientists study the world’s biggest problems in health and sustainability. By using this donated computing power, the scientists aim to identify promising chemical compounds for further laboratory testing.
The research team wants not only to help find treatments for COVID-19, but also to create a fast-response, open source toolkit that will help all scientists quickly search for treatments for future pandemics.
- nice! 🙂 release the sources!
- And in keeping with World Community Grid’s open data policy, all data and tools that are developed through this project will be shared freely in the scientific community.The project’s primary goal is to search for potential treatments for COVID-19, so studying proteins from SARS-CoV2 (the virus that causes COVID-19) is the highest priority.
- Additionally, scientists want to fight not only the current emergency, but also prepare for the ones that will likely follow.
- Future pandemics could stem from a progressive accumulation of mutations, which can eventually lead to a new virus variant.
- This is what happened when the virus SARS-CoV1 mutated to become SARS-CoV2. So, the research team is including proteins from the SARS-CoV1 and other viruses to be studied as part of OpenPandemics –COVID-19, which will help them assess how difficult would it be to find or design molecules capable of overcoming the inevitable mutations.
- Scripps Research, previously known as The Scripps Research Institute (or TSRI) is a nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in La Jolla, California with a sister facility in Jupiter, Florida, the institute has over 200 laboratories employing 2,400 scientists, technicians, graduate students, and administrative and other staff, making it the largest private, non-profit biomedical research organization in the United States and among the largest in the world.The institute holds nearly 1,000 patents, produced 9 FDA-approved therapeutics, and has generated over 50 spin-off companies. According to the 2017 Nature Innovation Index, Scripps Research is the #1 most influential research institution in the world. The Scripps Research graduate program is ranked 10th nationally in the biological sciences, 5th for organic chemistry, and 2nd for biochemistry.
- (src: Wikipedia)
|Microbiome Immunity Project
- project website
- video presentation of project
Each of us have as many as 30 trillion bacteria living in and on our bodies. These bacteria, most of which live in our digestive systems, are part of a system called the human microbiome. Most of these bacteria are harmless or even beneficial. However, some have been implicated in diseases such as Type 1 diabetes, Crohn’s disease, and ulcerative colitis.
Recent technological advances are enabling scientists to explore the human microbiome in detail for the first time. As scientists gain a better understanding of the role of human microbiome in the development of disease, they will be able to find and create better diagnoses and treatments.
To better understand the roles played by the various bacteria in the human microbiome, scientists need to study the proteins produced by these bacteria, which are encoded in their genomes. The first step is to determine the physical structures (shapes) of the protein molecules coded by each bacteria’s genes. This is important because the physical structure of a protein determines its function.
Once the protein functions are determined, scientists can explore how the bacterial proteins react with each other, and determine which proteins play a role in any number of diseases. From these insights, scientists would be able to develop drugs to control those particular proteins and help treat diseases that originate in or are influenced by the human microbiome.
The scale of this research is enormous: the microbiome is comprised of about 3 million unique bacterial genes. By comparison, the human body has about 20,000 genes. To study the proteins corresponding to each of these genes would be a monumental task that is nearly impossible in a laboratory setting. Most of these proteins have therefore not been explored.
While using traditional laboratory techniques is infeasible for the scale of the problem, computational methods can also be used to predict the protein structures. However, doing this at scale requires significantly more computational power than is typically available to scientists. World Community Grid addresses this need by harnessing computing power donated by volunteers from all over the world.
The Microbiome Immunity Project is using the power of World Community Grid to accelerate this initial step of predicting protein structures of the human microbiome. Specifically, World Community Grid volunteers are using their computers’ unused processing power to run millions of virtual experiments, each predicting the structure of a protein.
The resulting data will be analyzed by the researchers to find the most likely structure for each of the proteins under study. The research team will make their data publicly available to other scientists, accelerating the advancement of scientific knowledge in this important new area of research.
The project is initially focusing on the genes found in the microbiome of the human gut, and on diseases which have already been shown to be associated with gut bacteria including type 1 diabetes, Crohn’s disease, and ulcerative colitis.
|Help Stop TB
|FightAIDS@Home – Phase 2
|Mapping Cancer Markers
Cancer still kills more people than COVID19 probably ever will.
- project website
- project video presentation
- Cancers, one of the leading causes of death worldwide, come in many different types and forms in which uncontrolled cell growth can spread to other parts of the body.
- Unchecked and untreated, cancer can spread from an initial site to other parts of the body and ultimately lead to death. The disease is caused by genetic or environmental changes that interfere with biological mechanisms that control cell growth. These changes, as well as normal cell activities, can be detected in tissue samples through the presence of their unique chemical indicators, such as DNA and proteins, which together are known as “markers.”
- Specific combinations of these markers may be associated with a given type of cancer.The pattern of markers can determine whether an individual is susceptible to developing a specific form of cancer, and may also predict the progression of the disease, helping to suggest the best treatment for a given individual. For example, two patients with the same form of cancer may have different outcomes and react differently to the same treatment due to a different genetic profile. While several markers are already known to be associated with certain cancers, there are many more to be discovered, as cancer is highly heterogeneous.
- Mapping Cancer Markers on World Community Grid aims to identify the markers associated with various types of cancer. The project is analyzing millions of data points collected from thousands of healthy and cancerous patient tissue samples. These include tissues with lung, ovarian, prostate, pancreatic and breast cancers. By comparing these different data points, researchers aim to identify patterns of markers for different cancers and correlate them with different outcomes, including responsiveness to various treatment options.
This knowledge can help researchers and physicians to:
• Improve and personalize cancer treatment: by making it possible to detect cancer earlier, identify high-risk patients, and to customize treatment based on a patient’s personal genetic profile.
• Accelerate cancer research and improve the overall process for identifying markers: by refining the process of identifying markers, researchers can determine an individual patient’s markers more easily, and future large sets of data can be analyzed more efficiently.
Follow this project:
- May 2014 update
- Thomson Reuters Highly Cited Researchers list, 2014
- Media Coverage:
- Global PC network gives researchers supercomputer power, Massive global network of home and business computers linked to give researchers supercomputer power, The Star, Sep. 21 2014
- Canadian researcher wants home computers to find cancer cure, Metro News, September 21, 2014
- Global computer network powers research. The World Community Grid makes cancer research faster and more efficient, The Varsity, Vol CXXXV, No. 06, October 5
- October 2014 update
- February 2015 update
- June 2015 update
– Media coverage: Signs of intelligent biomarkers, DDNews, February 2015. http://www.ddn-news.com/index.php?newsarticle=9227
- November 2015 update
- September 2016 update
- March 2017 update
- November 2017 update
- July 2018 update
- December 2019 update
DrSc in Medical Sciences, Slovak Academy of Sciences, Bratislava, Slovakia
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