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Transcriptic Aims to Make the Biology Lab Programmable - Bio-IT World

Transcriptic Aims to Make the Biology Lab Programmable - Bio-IT World | Complex Insight  - Understanding our world | Scoop.it
Bio-IT World
Transcriptic Aims to Make the Biology Lab Programmable
Bio-IT World
At a time when monkeys are exerting telepathic control over mechanical limbs, most biologists still don't have access to robotics for even the simplest procedures.
ComplexInsight's insight:

Transcriptic is an awesomely promising start up - that aims to provide automated execution of different lab protocols.  Intersting article at Bio-IT World. If you are interested in the future of weblab work and how it connects to synthetic biology and bio discovery - well worth reading.

 

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bioinformatics-databases

bioinformatics-databases | Complex Insight  - Understanding our world | Scoop.it
Bioinformatics - Databases
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Dr.Stefan Gruenwalds scoop-it list of bioinformatics databases is an essential resource for anyone looking to discover which datasets are available and accessible. Awesome.

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Advances in Artificial Life, ECAL 2013 Proceedings

Advances in Artificial Life, ECAL 2013 Proceedings | Complex Insight  - Understanding our world | Scoop.it

ECAL 2013, the twelfth European Conference on Artificial Life, presents the current state of the art of a mature and autonomous discipline collocated at the intersection of a theoretical perspective (the scientific explanations of different levels of life organizations, e.g., molecules, compartments, cells, tissues, organs, organisms, societies, collective and social phenomena) and advanced technological applications (bio-inspired algorithms and techniques to building-up concrete solutions such as in robotics, data analysis, search engines, gaming).

 

Advances in Artificial Life, ECAL 2013

Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems

Edited by Pietro Liò, Orazio Miglino, Giuseppe Nicosia, Stefano Nolfi and Mario Pavone

http://mitpress.mit.edu/books/advances-artificial-life-ecal-2013


Via Complexity Digest
ComplexInsight's insight:

I have a big soft spot for artificial life research - partly because i was a young researcher  shortly after Chris Langton coined the term and a lot of my early hacking was around games of life, vants and cellular automata but also because over the years I have found many of the techniques discussed in ALIFE circles applicable to other fields such as machine learning, control architectures, and emergent simulation etc so this is definitely one for the reading list.

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luiy's curator insight, September 9, 2013 1:35 PM
About the Editors

 

Pietro Liò is Reader in Computational Biology at the University of Cambridge and a member of the Artificial Intelligence group of the University's Computer Laboratory. He researches on Predictive models in Personalized medicine and Multiscale modelling of molecules-cell-tissue-organ interactions.

 

 

Orazio Miglino is a full Professor of Psychology at University of Naples Federico II where he leads the Natural and Artificial Cognition Lab. He is also an associate researcher at the Institute of Cognitive Sciences and Technologies of Italian National Research Council (ISTC-CNR) in Rome.

 

 

Giuseppe Nicosia is an Associate Professor in Computational Systems and Synthetic Biology in the Dept. of Mathematics and Computer Science of the University of Catania, Italy. His research activities focus on the design of biological systems, neuroinformatics, system design, design automation, optimization, solar cells, circuit and semiconductor design.

 

 

Stefano Nolfi is Research Director at the Italian National Research Council (CNR), director of the Laboratory of Autonomous Robots and Artificial Life of the Institute of Cognitive Sciences and Technologies. His research activities focus on the evolution and development of behavioural and cognitive skills in natural and artificial embodied agents (robots).

 

 

Mario Pavone is an Assistant Professor in computer science at the Department of Mathematics and Computer Science of the University of Catania. He is co-founder of TaoScience Research center, and he is also a member of the EURO association (The Association of European Operational Research Societies)

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Researchers glimpse microbial 'dark matter'

Researchers glimpse microbial 'dark matter' | Complex Insight  - Understanding our world | Scoop.it

Led by Tanja Woyke, a microbiologist at the US Department of Energy’s Joint Genome Institute in Walnut Creek, California, researchers used single-cell sequencing to read the genomes of 201 bacterial and archaeal cells taken from nine diverse environments, such as hydrothermal vents and an underground gold mine. None of the organisms had ever been sequenced or cultivated in a laboratory. The results are published today in Nature1.

ComplexInsight's insight:

The ability to use single cell sequencing gives a whole new insight into microbial and bacterial worlds. The research highlights not only how we will be reassessing our definitions and classifications of bacterial and archaeal kingdoms but also the range of adaptations that wait to be discovered.

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Evolution of Mammalian Diving Capacity Traced by Myoglobin Net Surface Charge

Evolution of Mammalian Diving Capacity Traced by Myoglobin Net Surface Charge | Complex Insight  - Understanding our world | Scoop.it
Evolution of Mammalian Diving Capacity Traced by Myoglobin Net Surface Charge
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A new study published in Science shows marine mammals evolutionary adaptations to store oxygen for deep dives.  Extended breath-hold endurance enabled marine mammals to expand their range and ecological niche. However to achieve this their bodies have had to evolve mechanisms to store elevated body oxygen and use it hyper efficiently.The new study highlights the molecular and biochemical adaptations to marine mammal muscle myoglobin to enable extended dive capacity. Worth reading

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Will 'big data' prevent disease?

Will 'big data' prevent disease? | Complex Insight  - Understanding our world | Scoop.it
How the blistering pace of technological change could have a profound impact on healthcare.
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The combination of sensors and automated tests in areas of genetics and proteomics enable collection of largescale comprehensive health data for the first time. That data will generate insights into human biology, our bacterial biome and how our health systems work. Advances in large scale data processing, correlation and machine learning will help over the next decade to  radically change our understanding of human biology. As data is collected and in silico experimentation mapped to invitrio understanding data will change our  healthcare systems over the next 30 years.  This BBC article gives a good insight into how and why this is starting to happen now.

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DNA folded into shapes offers alternative gene delivery vehicle

DNA folded into shapes offers alternative gene delivery vehicle | Complex Insight  - Understanding our world | Scoop.it

Researchers from Johns Hopkins and Northwestern universities have discovered how to control the shape of nanoparticles that move DNA through the body and have shown that the shapes of these carriers may make a big difference in how well they work in treating cancer and other diseases.  The use of computer models allowed Luijten’s team to mimic traditional lab experiments at a far faster pace. These molecular dynamic simulations were performed on Quest, Northwestern’s high-performance computing system. The computations were so complex that some of them required 96 computer processors working simultaneously for one month.  “Our computer simulations and theoretical model have provided a mechanistic understanding, identifying what is responsible for this shape change,” Associate Professor Eric Luijten said. “We now can predict precisely how to choose the nanoparticle components if one wants to obtain a certain shape.”. Click on the image or the title to learn more.

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Gene Regulation I Lab Protocol | Intro Biology

Gene Regulation I Lab Protocol | Intro Biology | Complex Insight  - Understanding our world | Scoop.it

Simulation is increasingly used in biology to explore system relationships. This lab will gives students the opportunity to explore the regulation of bacterial gene expression through the use of both traditional biochemical lab techniques and modern computer simulations. While they incubate their bacteria, they use computer simulations to better understand how beta-galactosidase expression is regulated in E. coli. Thw dynamic model helps them make predictions as to the outcome of the experiment. There are computer simulations for different types of gene regulatory systems to explore and make predictions about how gene expression is controlled in each circumstance. Biology lessons were always cool - but they just got a whole lot cooler. Click on the image or headline to learn more. 

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Informatics, Biology Team Demonstrates Role of Foreign DNA Strands in Life-Supporting Bacteria

From - Lab Manager Magazine® : An Indiana University team of researchers has conducted the most in-depth and diverse genetic analysis of the defense systems that trillions of micro-organisms in the human body use to fend off viruses. Led by IU Bloomington assistant professor of informatics and computing Yuzhen Ye, the team of bioinformaticists and biologists reconstructed arrays of clusters of regularly interspaced short palindromic repeats -- CRISPRs -- which function as immune systems to the bacteria that play a vital role in human health. Between genomic repeats, CRISPR locations carry short strands of foreign DNA called spacers, which provide a history of past exposures to outside invaders like plasmids and bacteriophages (viruses that infect bacteria), and allow the bacteria to fight off viruses they have already encountered. This is an incredibly interesting piece of research and demonstrates the applications of CRISPRs to tracing the virus exposure of individuals  and it indicates the importance of effective identification and characterization of CRISPR loci to the study of the dynamic ecology of microbiomes and human health.  Learn more...

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Cell membrane is patterned like a patchwork quilt

Cell membrane is patterned like a patchwork quilt | Complex Insight  - Understanding our world | Scoop.it

(Phys.org) -- As the interface between the cell and its environment, the cell membrane, which consists of fats and proteins, fulfils a variety of vital functions. Scientists at the Max Planck Institute of Biochemistry in Martinsried near Munich have performed the first comprehensive analysis of the molecular structure of this boundary layer, and revealed precisely how it is organised. In yeast cells, the entire membrane is made up of independent domains, each containing just one or a few protein types. If a protein is relocated to an inappropriate domain, it may even fail to function. The study shows that the membrane is a kind of patchwork quilt and should help scientists to gain a better understanding of basic cellular processes. Learn more...

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Bio-Linux 6 ~ Bioinformatics made Simple

Bio-Linux 6 ~ Bioinformatics made Simple | Complex Insight  - Understanding our world | Scoop.it
Bio-Linux is an operating system set up for bioinformatics with a vast number of programs pre-installed. It can be obtained for free from the NERC Environmental Bioinformatics Centre. You can obtain a USB drive from NERC and boot from that ...

Via Dr Richard Badge
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What Comes After Antibiotics? 5 Alternatives to Stop Superbugs

What Comes After Antibiotics? 5 Alternatives to Stop Superbugs | Complex Insight  - Understanding our world | Scoop.it
"Superbug" bacterial infections that are resistant to common antibiotics are increasing at an alarming rate. But traditional antibiotics aren't the only way to battle dangerous germs. Biomedical scientists are investigating new additions to their arsenal.
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Given the WHO announcement that antibacterial resistance is now a global threat - article on popular mechanic outlines some of the alternate treatments to antibiotics.

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FANTOM

FANTOM | Complex Insight  - Understanding our world | Scoop.it
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In our bodies every cell contains the same genetic code, however the active or expressed genes determine cell function.  Which genes are expressed is controlled by tiny bits of the genome called promoters and enhancers and different cell types are determined by different combinations of promoters and enhancers. Now an international consortium of researchers known as FANTOM, led by the RIKEN institute in Japan have created the  clearest map yet of how genes control cells to make our bodies function. The map is already challenging ideas about what our genes do and how they interact and may accelerate the development of gene-based therapies. The team examined more than 800 human tissue samples, covering nearly all cell types, and  found 44,000 enhancers and 180,000 promoters that control gene expression.

 

 

 

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New virus 'not following Sars' path'

New virus 'not following Sars' path' | Complex Insight  - Understanding our world | Scoop.it
The new Mers virus, which has killed half of those infected, is "unlikely" to reach the same scale as Sars, ministers in Saudi Arabia say.
ComplexInsight's insight:

The source of the Mers virus is still unknown. Given that Mers is from the same group of viruses as Sars and Common Cold - understanding the genotype and phenotype differences and how they relate to pathogenic and vector pathways  in its related family could help to better understand both Mers and related groups and perhaps indicate a source. Viral evolution is something we still know relatively little about - and understanding of how they coevolve and relate to microbial habitat are becoming increasingly important to health planning and treatments.

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Genomics: The single life

Genomics: The single life | Complex Insight  - Understanding our world | Scoop.it
Sequencing DNA from individual cells is changing the way that researchers think of humans as a whole.
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Human genomes such as cancer have been traditionally sequenced from DNA extracted from multiple cells. With certain cancers we know that local individual cellular adaptations, mutations and variation impact gene expression, cell behaviour and drug response.  Nicholas Navin pioneered a new approach for single cell sequencing pioneered  in order to sequence individual cancer cells and map local mutations and adaptations. Timour Basian and team inspired by Navin's work, helped perfect techniques for single cell sequencing while dramatically reduced sequencing pricing from $1000 per single cell to approx $60 per cell.  The article discuses further developments, implications and potential opportunities created by the advent of single cell sequencing. Worth reading.

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Researchers identify key cellular organelle involved in gene silencing

Researchers identify key cellular organelle involved in gene silencing | Complex Insight  - Understanding our world | Scoop.it

Present in almost in every cell, microRNAs are known to target tens to hundreds of genes each and to be able to repress, or "silence," their expression. What is less well understood is how exactly miRNAs repress target gene expression. Now a team of scientists led by geneticists at the University of California, Riverside has conducted a study on plants (Arabidopsis) that shows that the site of action of the repression of target gene expression occurs on the endoplasmic reticulum (ER), a cellular organelle that is an interconnected network of membranes—essentially, flattened sacs and branching tubules—that extends like a flat balloon throughout the cytoplasm in plant and animal cells

ComplexInsight's insight:

I think this is fundamentally important. As a programmer - microRNA reminds me of microcode running on multiple parallel processes . With this work showing that ER membranes are essential for microRNA activity. The last line of the article nails it: "Our work shows that an integral membrane protein, AMP1, is required for the miRNA-mediated target gene repression to be successful. As AMP1 has counterparts in animals, our findings in plants could have broader implications." Full paper in Cell 

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ROSALIND | #bioinformatics #online #education

ROSALIND | #bioinformatics #online #education | Complex Insight  - Understanding our world | Scoop.it

Learning bioinformatics usually requires solving computational problems of varying difficulty that are extracted from real challenges of molecular biology.

To make learning bioinformatics fun and easy, we have founded Rosalind, a platform for learning bioinformatics through problem solving.

Rosalind offers an array of intellectually stimulating problems that grow in biological and computational complexity; each problem is checked automatically, so that the only resource required to learn bioinformatics is an internet connection.

Rosalind also promises to facilitate improvements in standard bioinformatics education by providing a vital teaching aid and a central homework resource.


Via Chris Upton + helpers
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Researcher will push emerging field of biodiversity informatics in Africa

Researcher will push emerging field of biodiversity informatics in Africa | Complex Insight  - Understanding our world | Scoop.it

Biodiversity informatics is about how to develop, integrate and use information about life on Earth,” said Town Peterson, University Distinguished Professor of Ecology and Evolutionary Biology and curator in the Biodiversity Institute. “We have a lot of raw data about biodiversity, which is to say we know places where particular species have been seen. But turning those raw data into usable information is a much bigger challenge.” In Africa, as in much of the world, there is scant availability of training in this important discipline. This is about to change. With funding from the JRS Biodiversity Foundation, Peterson will lead multiple training sessions in four African nations: Ghana, South Africa, Kenya and Egypt. CLick on image or title to learn more.

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Flu immunity is affected by how many viruses actually cause the infection

Flu immunity is affected by how many viruses actually cause the infection | Complex Insight  - Understanding our world | Scoop.it

Both the number of viruses in initial flu infection, and the virus type, affects the patient's outcome. Mice infected by high concentrations developed immunity, and generated immune cells in the lungs to fight other strains. Mice that were infected with a relatively low concentration of the virus developed weaker immunity against the strain that infected them, did not build up this crucial population of immune cells in the lungs, and showed only delayed immunity toward other flu strains. This discovery could pave the way for new prophylactic strategies to fight flu infections and provides a novel basis for vaccine design. Learn more by clicking on the image or headline.

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Researchers watch tiny living machines self-assemble

Researchers watch tiny living machines self-assemble | Complex Insight  - Understanding our world | Scoop.it

All crea­tures, from bac­te­ria to hu­mans, mon­i­tor and trans­form their en­vi­ron­ments us­ing small pro­tein nano­ma­chines made of thou­sands of atoms,” ex­plained the sen­ior au­thor of the stu­dy, Ste­phen Mich­nick of the Uni­vers­ity of Mont­real de­part­ment of bio­chem­is­try. To un­der­stand how a pro­tein goes from a lin­ear chain to a un­ique as­sem­bled struc­ture, Michnik's team de­vel­oped a strat­e­gy to mon­i­tor pro­tein as­sembly by in­te­grat­ing flu­o­res­cent probes through­out the lin­ear pro­tein chain so that they could de­tect the struc­ture of each stage of pro­tein as­sembly, step by step to its fi­nal struc­ture. Learn more...

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mBiosphere: Commentary: Black Queen Hypothesis sheds light on evolution of complexity

mBiosphere: Commentary: Black Queen Hypothesis sheds light on evolution of complexity | Complex Insight  - Understanding our world | Scoop.it

mBio is a great source for developments in biology. This week they have a good commentary on the Sachs and Hollowell Black Queen hypothesis which has implications for how we understand the evolution of bacterial genomes and for the development of new techniques for growing bacteria in the lab.  Learn More...

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Open-data project aims to ease the way for genomic research

Open-data project aims to ease the way for genomic research | Complex Insight  - Understanding our world | Scoop.it

This one is important to us as we start testing OLAPX and BIOLAP approaches for data analysis.  The Ewing Marion Kauffman Foundation, based in Kansas City, Missouri,  aims to “create the world’s largest pool of openly available, user-contributed data about health and genomics” in hopes of easing challenges with informed consent and data ownership that some biomedical researchers say are holding science back in the era of ‘big data’. Learn more...

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