Scientists at the Technion-Israel Institute of Technology have developed an advanced biological transducer that is capable of manipulating genetic codes and using computational outputs as new inputs. This DNA-based transducer can iteratively compute and produce biologically relevant results. It offers benefits like reading and transforming genetic information at the molecular scale and interacting directly with living organisms. The transducer could be used to evaluate, detect, alter, and process genetic sequences, demonstrating a novel synthetic biological computing machine.
Introduction to Systemics with focus on Systems BiologyMrinal Vashisth
The core content discusses the terminology used in Systems Sciences, the systems thinking/approach or Systemics. Focus is kept on Systems Biology for the most part of the presentations where it is compared with other disciplines and examples of Systems Biology approach and challenges of systems science are also discussed.
The sad thing about uploading this to Slide Share is that animations don't work.
Computational Biology and Bioinformatics pact with application of computers in solving problems of molecular biology. Computational biology stretches several classical areas such as biology, physics, chemistry, computer science, statistics and, and the activities in the area are numerous.
The area of computational biology is also indicated to as bioinformatics. These two names are used interchangeably, but there seems to be a consensus forming where computational biology is used to indicate to activities which mainly indicates on constructing algorithms that address problems with biological purpose, while bioinformatics is used to refer to activities which mainly target on constructing and using computational technique to analyze possible biological data.
Visualization and Analysis of Dynamic Networks Alexander Pico
DynNetwork development was taken up initially by Sabina Sara Pfister back in GSoC 2012. She laid out a strong foundation for dynamic network visualization in Cytoscape and my job was to extend the plugin’s functionality to help users analyse time changing networks. The two of us were mentored by Jason Montojo. We had developed a decent tool over the course of two GSoC programs to aid dynamic network analysis and our efforts culminated in DynNetwork getting accepted for an oral presentation at the International Network for Social Network Analysis (INSNA), Sunbelt 2014 which was held in St. Petersburg, FL in February.
Introduction to Systemics with focus on Systems BiologyMrinal Vashisth
The core content discusses the terminology used in Systems Sciences, the systems thinking/approach or Systemics. Focus is kept on Systems Biology for the most part of the presentations where it is compared with other disciplines and examples of Systems Biology approach and challenges of systems science are also discussed.
The sad thing about uploading this to Slide Share is that animations don't work.
Computational Biology and Bioinformatics pact with application of computers in solving problems of molecular biology. Computational biology stretches several classical areas such as biology, physics, chemistry, computer science, statistics and, and the activities in the area are numerous.
The area of computational biology is also indicated to as bioinformatics. These two names are used interchangeably, but there seems to be a consensus forming where computational biology is used to indicate to activities which mainly indicates on constructing algorithms that address problems with biological purpose, while bioinformatics is used to refer to activities which mainly target on constructing and using computational technique to analyze possible biological data.
Visualization and Analysis of Dynamic Networks Alexander Pico
DynNetwork development was taken up initially by Sabina Sara Pfister back in GSoC 2012. She laid out a strong foundation for dynamic network visualization in Cytoscape and my job was to extend the plugin’s functionality to help users analyse time changing networks. The two of us were mentored by Jason Montojo. We had developed a decent tool over the course of two GSoC programs to aid dynamic network analysis and our efforts culminated in DynNetwork getting accepted for an oral presentation at the International Network for Social Network Analysis (INSNA), Sunbelt 2014 which was held in St. Petersburg, FL in February.
This talk discusses collaboration challenges in the context of three projects: the Protégé Ontology Editor, the BioPortal ontology repository, and the CEDAR metadata management system
Systems biology is the computational and mathematical modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach (holism instead of the more traditional reductionism) to biological research.
Computational Approaches to Systems BiologyMike Hucka
Presentation given at the Sydney Computational Biologists meetup on 21 August 2013 (http://australianbioinformatics.net/past-events/2013/8/21/computational-approaches-to-systems-biology.html).
Systems biology & Approaches of genomics and proteomicssonam786
This presentation provides the basic understanding of varous genomics and proteomics techniques.Systems biology studies life as a system .It includes the study of living system using various omic technologies .
Presentation for Network Biology SIG 2013 by Gang Su, University of Michigan, USA. “CoolMap Cytoscape App: Flexible Multi-scale Heatmap-Driven Molecular Network Exploration”
Network approaches have generated substantial interest based on their great potential for integrative omics analysis and are expected to facilitate a new era of precision understanding of complex diseases
Week 1 lecture for High School Bioinformatics course; covers why we need to use computers in biology, what bioinformatics/computational biology is, an introduction to machine learning, and examples from current research
This talk discusses collaboration challenges in the context of three projects: the Protégé Ontology Editor, the BioPortal ontology repository, and the CEDAR metadata management system
Systems biology is the computational and mathematical modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach (holism instead of the more traditional reductionism) to biological research.
Computational Approaches to Systems BiologyMike Hucka
Presentation given at the Sydney Computational Biologists meetup on 21 August 2013 (http://australianbioinformatics.net/past-events/2013/8/21/computational-approaches-to-systems-biology.html).
Systems biology & Approaches of genomics and proteomicssonam786
This presentation provides the basic understanding of varous genomics and proteomics techniques.Systems biology studies life as a system .It includes the study of living system using various omic technologies .
Presentation for Network Biology SIG 2013 by Gang Su, University of Michigan, USA. “CoolMap Cytoscape App: Flexible Multi-scale Heatmap-Driven Molecular Network Exploration”
Network approaches have generated substantial interest based on their great potential for integrative omics analysis and are expected to facilitate a new era of precision understanding of complex diseases
Week 1 lecture for High School Bioinformatics course; covers why we need to use computers in biology, what bioinformatics/computational biology is, an introduction to machine learning, and examples from current research
Biocomputing is an interdisciplinary research area which combines biology, computer science, and engineering. It is the process of building computers that use biological materials. It uses systems of biologically derived molecules, such as proteins and DNA, to perform computational calculations. This paper provides a brief introduction to biocomputing. Matthew N. O. Sadiku | Nana K. Ampah | Sarhan M. Musa "Biocomputing" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-2 | Issue-6 , October 2018, URL: http://www.ijtsrd.com/papers/ijtsrd18825.pdf
In this deck from the 2014 HPC User Forum in Seattle, Jack Collins from the National Cancer Institute presents: Genomes to Structures to Function: The Role of HPC.
Watch the video presentation: http://wp.me/p3RLHQ-d28
The Impact of Information Technology on Chemistry and Related SciencesAshutosh Jogalekar
This is a copy of an invited talk I gave at the ACS meeting in Dallas in March 2014. The talk was about the impact of information technology on chemistry and related sciences. I interpreted 'information technology' broadly and divided the talk into three sections: Data, Simulation and Sociology.
'Data' talks about how chemical information has grown exponentially and how chemists are coming up with new techniques to store, organize and understand this information.
'Simulation' talks about how chemists are using the last two decades' spectacular progress in hardware and software to understand the behavior of molecules in a variety of applications ranging from drug design to new materials.
'Sociology' talks about the impact of blogs and social media on the practice of chemistry. More specifically I talk about how social media is serving as a 'second tier' of peer review and how this new medium is having an increasingly influential impact on many issues close to chemists' hearts including lab safety, 'chemophobia' and the public appreciation of chemistry.
Tales from BioLand - Engineering Challenges in the World of Life SciencesStefano Di Carlo
Prof. Alfredo Benso from SysBio Group @ Politecnico di Torino keynote presentation at ICIIBMS - IEEE International Conference on Intelligent Informatics and BioMedical Sciences, on Nov 26 2017 in Okinawa (Japan).
Future Directions in Chemical Engineering and BioengineeringIlya Klabukov
"Future Directions in Chemical Engineering and Bioengineering"
January 16-18, 2013
Austin, Texas
Chair: John G. Ekerdt, The University of Texas at Austin
Sponsored by Department of Defense,
Office of the Assistant Secretary of Defense for Research and Engineering
Chemical and biological engineers use math, physics, chemistry, and biology to develop chemical transformations and processes, creating useful products and materials that improve society. In recent years, the boundaries between chemical engineering and bioengineering have blurred as biology has become molecular science, more seamlessly connecting with the historic focus of chemical engineering on molecular interactions and transformations.
This disappearing boundary creates new opportunities for the next generation of engineered systems – hybrid systems that integrate the specificity of biology with chemical and material systems to enable novel applications in catalysis, biomaterials, electronic materials, and energy conversion materials.
Basic research for the U.S. Department of Defense covers a wide range of topics such as metamaterials and plasmonics, quantum information science, cognitive neuroscience, understanding human behavior, synthetic biology, and nanoscience and nanotechnology. Future Directions workshops such as this one identify opportunities
for continuing and future DOD investment. The intent is to create conditions for discovery and transformation, maximize the discovery potential, bring balance and coherence, and foster connections. Basic research stretches the limits of today’s technologies and discovers new phenomena and know-how that ultimately lead to future technologies and enable military and societal progress.
The Dawn of the Age of Artificially Intelligent NeuroprostheticsSagar Hingal
A summary or an overview of the existing technologies that encapsulate the concepts of NeuroScience and Bio-Technology using the enhanced methods of Artificial-intelligence.
In this review paper, there are several case studies and methodologies of implementations of neuroprosthetics as well as how A.I (Artificial Intelligence) is evolved over the period of time and what is next on the future.....
NanoAgents: Molecular Docking Using Multi-Agent TechnologyCSCJournals
Traditional computer-based simulators for manual molecular docking for rational drug discovery have been very time consuming. In this research, a multi agent-based solution, named as NanoAgent, has been developed to automate the drug discovery process with little human intervention. In this solution, ligands and proteins are implemented as agents who pose the knowledge of permitted connections with other agents to form new molecules. The system also includes several other agents for surface determination, cavity finding and energy calculation. These agents autonomously activate and communicate with each other to come up with a most probable structure over the ligands and proteins, which are participating in deliberation. Domain ontology is maintained to store the common knowledge of molecular bindings, whereas specific rules pertaining to the behaviour of ligands and proteins are stored in their personal ontologies. Existing, Protein Data Bank (PDB) has also been used to calculate the space required by ligand to bond with the receptor. The drug discovery process of NanoAgent has exemplified exciting features of multi agent technology, including communication, coordination, negotiation, butterfly effect, self-organizing and emergent behaviour. Since agents consume fewer computing resources, NanoAgent has recorded optimal performance during the drug discovery process. NanoAgent has been tested for the discovery of the known drugs for the known protein targets. It has 80% accuracy by considering the prediction of the correct actual existence of the docked molecules using energy calculations. By comparing the time taken for the manual docking process with the time taken for the molecular docking by NanoAgent, there has been 95% efficiency.
NanoAgents: Molecular Docking Using Multi-Agent Technology
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1. Advanced Biological Computer Developed
May 23, 2013 — Using only biomolecules (such as DNA and enzymes), scientists at the Technion-
Israel Institute of Technology have developed and constructed an advanced biological
transducer, a computing machine capable of manipulating genetic codes, and using the output
as new input for subsequent computations. The breakthrough might someday create new
possibilities in biotechnology, including individual gene therapy and cloning.
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The findings appear today (May 23, 2013) in Chemistry & Biology (Cell Press).
Interest in such biomolecular computing devices is strong, mainly because of their ability (unlike
electronic computers) to interact directly with biological systems and even living organisms. No
interface is required since all components of molecular computers, including hardware,
software, input and output, are molecules that interact in solution along a cascade of
programmable chemical events.
"Our results show a novel, synthetic designed computing machine that computes iteratively and
produces biologically relevant results," says lead researcher Prof. Ehud Keinan of the Technion
Schulich Faculty of Chemistry. "In addition to enhanced computation power, this DNA-based
transducer offers multiple benefits, including the ability to read and transform genetic
information, miniaturization to the molecular scale, and the aptitude to produce computational
results that interact directly with living organisms."
The transducer could be used on genetic material to evaluate and detect specific sequences,
and to alter and algorithmically process genetic code. Similar devices, says Prof. Keinan, could be
applied for other computational problems.
"All biological systems, and even entire living organisms, are natural molecular computers. Every
one of us is a biomolecular computer, that is, a machine in which all components are molecules
"talking" to one another in a logical manner. The hardware and software are complex biological
molecules that activate one another to carry out some predetermined chemical tasks. The input
is a molecule that undergoes specific, programmed changes, following a specific set of rules
(software) and the output of this chemical computation process is another well defined
molecule."
Also contributing to the research were postdoctoral fellows Dr. Tamar Ratner and Dr. Ron Piran
of the Technion's Schulich Faculty of Chemistry, and Dr. Natasha Jonoska of the Department of
Mathematics at the University of South Florida.