View allAll Photos Tagged bioinformatics
Minna is an MBI student who was interviewed for the CS Department's blog and MBI web site.
Setup: Sunpak 383 + white shoot-through umbrella camera left, 430EX camera right, triggered with a CTR-301 (ebay) trigger.
Dr. Wajjaht Qazi
Assistant Professor, Department of Computer Science
He is an Assistant Professor, in the department of Computer Science at COMSATS Institute of Information Technology. He worked as DeputyDirector/Assistant Professor Department of Computer Science, GC University Lahore, Senior Scientific Officer Institute of Molecular Science and bioinformatics, Senior Lecturer Preston University, System Architect Intelli-Technologies, Assistant Project Manager Softedge and Assistant Project Manager National Engineers. His area of Interest includes Quantum Computing and Cognition, Cybernetics, Artificial General Intelligence, Machine Consciousness, Bioinformatics. He is the author of the book “Machine Learning in Bioinformatics: An Approach for Protein Sequence Analysis” and several Journal Papers.
He is also a TED Ed educator, He was recently invited by TED to be their educator, making him among the only 10 educators in Punjab
Bildet kan brukes med kreditering av fotograf Geir Mogen / NTNU
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If used, please credit Geir Mogen, NTNU
Pavel Pevzner, a pioneer and widely recognized leader in the field of computational molecular biology, or bioinformatics, whose focus on genome rearrangements—a common type of genetic mutation—has illuminated the study of both evolutionary history and cancer.
Dr. Brian Enquist, an expert in ecology and evolutionary biology, brings to life a geographic inventory of forest assets for western North America. When coupled with the latest climate models, a high-resolution picture emerges of the health of our future forests. New advances in bioinformatics and mathematical modeling enable us, for the first time, to answer the question ‘what will the forest in my backyard look like?’ This presentation, produced in concert with the local Aspen Center for Environmental Studies, is cutting edge both in analyses and technological interface, and will demonstrate what we will experience over the coming decades if action on a grander scale is not taken. The science of climate change and forest health is revealing potentially dramatic implications for all of us, whether we be homeowners, recreationists, investors, insurers, or land developers.
CRI Workshop Learning Series
Bioinformatics Workshop 2014
Harper Court, Chicago
Photo by Jorge Andrade
Workflow by Hannah Tipney
How Honduras managed to carry out genomic sequencing for the first time
June 2023
When microbiologist Soany Ávilez was selected to implement the genomic sequencing of the SARS-CoV-2 virus in Honduras, she was amazed. In the wake of the pandemic, Soany had started working at the National Virology Laboratory in 2020 performing PCR tests. At that time, genomic sequencing to detect circulating variants of the virus that causes COVID-19 was carried out outside the country. But a project to provide Honduras with the capabilities to do it in situ and obtain faster results was being developed with technical support from the Pan American Health Organization (PAHO) and financial support from the United States Government.
Although she lacked knowledge on the subject, Soany remembers that she longed for the opportunity to work in sequencing. "When they chose us (her and her partner Karla Romero) to implement sequencing in the country and move the area forward, I couldn't believe it," she says.
Genomic surveillance allows us to know the evolution of viruses and other pathogens as they change over time. Knowing those changes or mutations that can modify its transmissibility and severity, allows us to guide public health measures. During the pandemic, it was a key strategy to monitor the behavior of SARS-CoV-2 and a technique that is being integrated into the surveillance of other pathogens.
Karla Romero, the other microbiologist in charge of genomic surveillance, acknowledges that the implementation of sequencing in Honduras has been "a great challenge" that required a lot of "sacrifice and commitment" both inside and outside the laboratory.
The sequencing area had to be created from scratch. In 2022, the authorities selected and conditioned a space within the National Virology Laboratory. With the support of PAHO, a sequencer, supplies, reagents, and furniture were purchased, and Soany and Karla were trained in bioinformatics and genomic sequencing at the Gorgas Memorial Institute in Panama.
“All with the aim of strengthening the capacities for genomic surveillance of SARS-CoV-2 and other pathogens in Honduras,” says Gabriela Rodriguez Segura, coordinator of the PAHO Project for the Consolidation of Genomic Sequencing Capacities in Honduras. Before these capacities were created at the local level, samples to determine the variants circulating in the country were sent to the laboratories of the Regional Network for Genomic Surveillance of COVID-19 (COVIGEN) created by PAHO to support countries without capacity to carry out sequencing in its territory.
In March 2023, the effort paid off and excitement took over the National Virology Laboratory when, after several attempts, the first sequencing of SARS-COV-2 in the country was successfully carried out. “We couldn't believe it,” says Soany. "We feel very happy because it was a great challenge and the result made us feel fulfilled."
On March 21, 2023, the results were obtained and it was the first time that the XBB sublineage of the omicron variant was detected in the country and by Honduran health professionals. For Karla, the key was “not to give up in the face of the biggest challenge”.
"It is a milestone for the country that genomic sequencing is being carried out," says Dr. Mitzi Castro, head of the National Health Surveillance Laboratory of Honduras. “It is a historic moment because we are starting from here to carry out future genomic surveillance of other pathogens of sanitary interest to the country,” she adds.
According to Dr. Castro, the country now has state-of-the-art technology. "The laboratory is at the forefront, and that is a success and a source of pride, for which we thank all those who have contributed their bit so that Honduras is not left behind."
Howest plechtige Proclamatie Brugge - Bachelor Verpleegkunde, Brugopleiding Verpleegkunde, Bachelor Biomedische Laboratorium-technologie en Advanced Bachelor of Bioinformatics - 7 november 2024
Elements of Bioinformatics:
Yet another PTEP (Periodic Table of the Elements Parody). I often love
these, but this one is truly exceptional, because I love
bioinformatics tools, also. Now, yes, there are more bioinformatics
and genomics tools, but this is the cream of the crop, the best ones,
compiled into an interactive visual structure that facilitates easy
browsing by category and clear relationship for types of tools. The
largest grouping of tools are the open source tools, and the smallest
are commercial tools. Bravo, bravo! When you mouse over the "Key to
Tool Type", whichever category your mouse is on is highlighted across
all groupings. Click on an elemental symbol, and you get more
detailed information about the tool represented by that two-letter
code, including authors, operating system, year created, publication,
download (or more info) link, licensing. Excellent structure for the
metadata. Color me impressed, and delighted to find this awesome
useful tool.
How Honduras managed to carry out genomic sequencing for the first time
June 2023
When microbiologist Soany Ávilez was selected to implement the genomic sequencing of the SARS-CoV-2 virus in Honduras, she was amazed. In the wake of the pandemic, Soany had started working at the National Virology Laboratory in 2020 performing PCR tests. At that time, genomic sequencing to detect circulating variants of the virus that causes COVID-19 was carried out outside the country. But a project to provide Honduras with the capabilities to do it in situ and obtain faster results was being developed with technical support from the Pan American Health Organization (PAHO) and financial support from the United States Government.
Although she lacked knowledge on the subject, Soany remembers that she longed for the opportunity to work in sequencing. "When they chose us (her and her partner Karla Romero) to implement sequencing in the country and move the area forward, I couldn't believe it," she says.
Genomic surveillance allows us to know the evolution of viruses and other pathogens as they change over time. Knowing those changes or mutations that can modify its transmissibility and severity, allows us to guide public health measures. During the pandemic, it was a key strategy to monitor the behavior of SARS-CoV-2 and a technique that is being integrated into the surveillance of other pathogens.
Karla Romero, the other microbiologist in charge of genomic surveillance, acknowledges that the implementation of sequencing in Honduras has been "a great challenge" that required a lot of "sacrifice and commitment" both inside and outside the laboratory.
The sequencing area had to be created from scratch. In 2022, the authorities selected and conditioned a space within the National Virology Laboratory. With the support of PAHO, a sequencer, supplies, reagents, and furniture were purchased, and Soany and Karla were trained in bioinformatics and genomic sequencing at the Gorgas Memorial Institute in Panama.
“All with the aim of strengthening the capacities for genomic surveillance of SARS-CoV-2 and other pathogens in Honduras,” says Gabriela Rodriguez Segura, coordinator of the PAHO Project for the Consolidation of Genomic Sequencing Capacities in Honduras. Before these capacities were created at the local level, samples to determine the variants circulating in the country were sent to the laboratories of the Regional Network for Genomic Surveillance of COVID-19 (COVIGEN) created by PAHO to support countries without capacity to carry out sequencing in its territory.
In March 2023, the effort paid off and excitement took over the National Virology Laboratory when, after several attempts, the first sequencing of SARS-COV-2 in the country was successfully carried out. “We couldn't believe it,” says Soany. "We feel very happy because it was a great challenge and the result made us feel fulfilled."
On March 21, 2023, the results were obtained and it was the first time that the XBB sublineage of the omicron variant was detected in the country and by Honduran health professionals. For Karla, the key was “not to give up in the face of the biggest challenge”.
"It is a milestone for the country that genomic sequencing is being carried out," says Dr. Mitzi Castro, head of the National Health Surveillance Laboratory of Honduras. “It is a historic moment because we are starting from here to carry out future genomic surveillance of other pathogens of sanitary interest to the country,” she adds.
According to Dr. Castro, the country now has state-of-the-art technology. "The laboratory is at the forefront, and that is a success and a source of pride, for which we thank all those who have contributed their bit so that Honduras is not left behind."
Christopher L. Barrett, Executive Director, Virginia Bioinformatics Institute/Professor of Computer Science, Virginia Tech. Dr. Barrett’s talk entitled “Massively Interactive Systems: Thinking and Deciding in the Age of Big Data"
Abstract: This talk discusses advanced computationally assisted reasoning about large interaction-dominated systems. Current questions in science, from the biochemical foundations of life to the scale of the world economy, involve details of huge numbers and levels of intricate interactions. Subtle indirect causal connections and vastly extended definitions of system boundaries dominate the immediate future of scientific research. Beyond sheer numbers of details and interactions, the systems are variously layered and structured in ways perhaps best described as networks. Interactions include, and often co-create, these morphological and dynamical features, which can interact in their own right. Such “massively interacting” systems are characterized by, among other things, large amounts of data and branching behaviors. Although the amount of associated data is large, the systems do not even begin to explore their entire phase spaces. Their study is characterized by advanced computational methods. Major methodological revisions seem to be indicated.
Heretofore unavailable and rapidly growing basic source data and increasingly powerful computing resources drive complex system science toward unprecedented detail and scale. There is no obvious reason for this direction in science to change. The cost of acquiring data has historically dominated scientific costs and shaped the research environment in terms of approaches and even questions. In the several years, as the costs of social data, biological data and physical data have plummeted on a per-unit basis and as the volume of data is growing exponentially, the cost drivers for scientific research have clearly shifted from data generation to storage and analytical computation-based methods. The research environment is rapidly being reshaped by this change and, in particular, the social and bio–sciences are revolutionized by it. Moreover, the study of socially– and biologically–coupled systems (e.g., societal infrastructures and infectious disease public health policy analysis) is in flux as computation-based methods begin to greatly expand the scope of traditional problems in revolutionary ways.
How does this situation serve to guide the development of “information portal technology” for complex system science and for decision support? An example of an approach to detailed computational analysis of social and behavioral interaction with physical and infrastructure effects in the immediate aftermath of a devastating disaster will be described in this context.
How Honduras managed to carry out genomic sequencing for the first time
June 2023
When microbiologist Soany Ávilez was selected to implement the genomic sequencing of the SARS-CoV-2 virus in Honduras, she was amazed. In the wake of the pandemic, Soany had started working at the National Virology Laboratory in 2020 performing PCR tests. At that time, genomic sequencing to detect circulating variants of the virus that causes COVID-19 was carried out outside the country. But a project to provide Honduras with the capabilities to do it in situ and obtain faster results was being developed with technical support from the Pan American Health Organization (PAHO) and financial support from the United States Government.
Although she lacked knowledge on the subject, Soany remembers that she longed for the opportunity to work in sequencing. "When they chose us (her and her partner Karla Romero) to implement sequencing in the country and move the area forward, I couldn't believe it," she says.
Genomic surveillance allows us to know the evolution of viruses and other pathogens as they change over time. Knowing those changes or mutations that can modify its transmissibility and severity, allows us to guide public health measures. During the pandemic, it was a key strategy to monitor the behavior of SARS-CoV-2 and a technique that is being integrated into the surveillance of other pathogens.
Karla Romero, the other microbiologist in charge of genomic surveillance, acknowledges that the implementation of sequencing in Honduras has been "a great challenge" that required a lot of "sacrifice and commitment" both inside and outside the laboratory.
The sequencing area had to be created from scratch. In 2022, the authorities selected and conditioned a space within the National Virology Laboratory. With the support of PAHO, a sequencer, supplies, reagents, and furniture were purchased, and Soany and Karla were trained in bioinformatics and genomic sequencing at the Gorgas Memorial Institute in Panama.
“All with the aim of strengthening the capacities for genomic surveillance of SARS-CoV-2 and other pathogens in Honduras,” says Gabriela Rodriguez Segura, coordinator of the PAHO Project for the Consolidation of Genomic Sequencing Capacities in Honduras. Before these capacities were created at the local level, samples to determine the variants circulating in the country were sent to the laboratories of the Regional Network for Genomic Surveillance of COVID-19 (COVIGEN) created by PAHO to support countries without capacity to carry out sequencing in its territory.
In March 2023, the effort paid off and excitement took over the National Virology Laboratory when, after several attempts, the first sequencing of SARS-COV-2 in the country was successfully carried out. “We couldn't believe it,” says Soany. "We feel very happy because it was a great challenge and the result made us feel fulfilled."
On March 21, 2023, the results were obtained and it was the first time that the XBB sublineage of the omicron variant was detected in the country and by Honduran health professionals. For Karla, the key was “not to give up in the face of the biggest challenge”.
"It is a milestone for the country that genomic sequencing is being carried out," says Dr. Mitzi Castro, head of the National Health Surveillance Laboratory of Honduras. “It is a historic moment because we are starting from here to carry out future genomic surveillance of other pathogens of sanitary interest to the country,” she adds.
According to Dr. Castro, the country now has state-of-the-art technology. "The laboratory is at the forefront, and that is a success and a source of pride, for which we thank all those who have contributed their bit so that Honduras is not left behind."
Christopher L. Barrett, Executive Director, Virginia Bioinformatics Institute/Professor of Computer Science, Virginia Tech. Dr. Barrett’s talk entitled “Massively Interactive Systems: Thinking and Deciding in the Age of Big Data"
Abstract: This talk discusses advanced computationally assisted reasoning about large interaction-dominated systems. Current questions in science, from the biochemical foundations of life to the scale of the world economy, involve details of huge numbers and levels of intricate interactions. Subtle indirect causal connections and vastly extended definitions of system boundaries dominate the immediate future of scientific research. Beyond sheer numbers of details and interactions, the systems are variously layered and structured in ways perhaps best described as networks. Interactions include, and often co-create, these morphological and dynamical features, which can interact in their own right. Such “massively interacting” systems are characterized by, among other things, large amounts of data and branching behaviors. Although the amount of associated data is large, the systems do not even begin to explore their entire phase spaces. Their study is characterized by advanced computational methods. Major methodological revisions seem to be indicated.
Heretofore unavailable and rapidly growing basic source data and increasingly powerful computing resources drive complex system science toward unprecedented detail and scale. There is no obvious reason for this direction in science to change. The cost of acquiring data has historically dominated scientific costs and shaped the research environment in terms of approaches and even questions. In the several years, as the costs of social data, biological data and physical data have plummeted on a per-unit basis and as the volume of data is growing exponentially, the cost drivers for scientific research have clearly shifted from data generation to storage and analytical computation-based methods. The research environment is rapidly being reshaped by this change and, in particular, the social and bio–sciences are revolutionized by it. Moreover, the study of socially– and biologically–coupled systems (e.g., societal infrastructures and infectious disease public health policy analysis) is in flux as computation-based methods begin to greatly expand the scope of traditional problems in revolutionary ways.
How does this situation serve to guide the development of “information portal technology” for complex system science and for decision support? An example of an approach to detailed computational analysis of social and behavioral interaction with physical and infrastructure effects in the immediate aftermath of a devastating disaster will be described in this context.
It looks nifty, doesn't it? The cube is 12cm (5 inches) on all sides and made of bead blasted stainless steel.
The pro photographer is Sanne Berg - check her pictures out at www.sanneberg.dk
Howest plechtige Proclamatie Brugge - Bachelor Verpleegkunde, Brugopleiding Verpleegkunde, Bachelor Biomedische Laboratorium-technologie en Advanced Bachelor of Bioinformatics - 7 november 2024