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3quarksdaily: Synthetic Biology: Engineering Life To Examine It

3quarksdaily: Synthetic Biology: Engineering Life To Examine It | Modern Life Science: of computers and men | Scoop.it

Via Gerd Moe-Behrens, Pedro Fernandes
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From computing biology to biology for computing...!

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Gerd Moe-Behrens's curator insight, January 7, 2014 5:33 AM

by
Jalees Rehman

*Two scientific papers that were published in the journal Nature in the year 2000 marked the beginning of engineering biological circuits in cells. The paper "Construction of a genetic toggle switch in Escherichia coli" by Timothy Gardner, Charles Cantor and James Collins created a genetic toggle switch by simultaneously introducing an artificial DNA plasmid into a bacterial cell. This DNA plasmid contained two promoters (DNA sequences which regulate the expression of genes) and two repressors (genes that encode for proteins which suppress the expression of genes) as well as a gene encoding for green fluorescent protein that served as a read-out for the system. The repressors used were sensitive to either selected chemicals or temperature. In one of the experiments, the system was turned ON by adding the chemical IPTG (a modified sugar) and nearly all the cells became green fluorescent within five to six hours. Upon raising the temperature to activate the temperature-sensitive repressor, the cells began losing their green fluorescence within an hour and returned to the OFF state. Many labs had used chemical or temperature switches to turn gene expression on in the past, but this paper was the first to assemble multiple genes together and construct a switch which allowed switching cells back and forth between stable ON and OFF states.

 Dna-163466_640 The same issue of Nature contained a second land-mark paper which also described the engineering of gene circuits. The researchers Michael Elowitz and Stanislas Leibler describe the generation of an engineered gene oscillator in their article "A synthetic oscillatory network of transcriptional regulators". By introducing three repressor genes which constituted a negative feedback loop and a green fluorescent protein as a marker of the oscillation, the researchers created a molecular clock in bacteria with an oscillation period of roughly 150 minutes. The genes and proteins encoded by the genes were not part of any natural biological clock and none of them would have oscillated if they had been introduced into the bacteria on their own. The beauty of the design lay in the combination of three serially repressing genes and the periodicity of this engineered clock reflected the half-life of the protein encoded by each gene as well as the time it took for the protein to act on the subsequent member of the gene loop.  Both papers described the introduction of plasmids encoding for multiple genes into bacteria but this itself was not novel. In fact, this has been a routine practice since the 1970s for many molecular biology laboratories. The panache of the work lay in the construction of functional biological modules consisting of multiple genes which interacted with each other in a controlled and predictable manner. Since the publication of these two articles, hundreds of scientific papers have been published which describe even more intricate engineered gene circuits. These newer studies take advantage of the large number of molecular tools that have become available to query the genome as well as newer DNA plasmids which encode for novel biosensors and regulators. Synthetic biology is an area of science devoted to engineering novel biological circuits, devices, systems, genomes or even whole organisms. This rather broad description of what "synthetic biology" encompasses reflects the multidisciplinary nature of this field which integrates ideas derived from biology, engineering, chemistry and mathematical modeling as well as a vast arsenal of experimental tools developed in each of these disciplines. Specific examples of "synthetic biology" include the engineering of microbial organisms that are able to mass produce fuels or other valuable raw materials, synthesizing large chunks of DNA to replace whole chromosomes or even the complete genome in certain cells, assembling synthetic cells or introducing groups of genes into cells so that these genes can form functional circuits by interacting with each other. Synthesis in the context of synthetic biology can signify the engineering of artificial genes or biological systems that do not exist in nature (i.e. synthetic = artificial or unnatural), but synthesis can also stand for integration and composition, a meaning which is closer to the Greek origin of the word.  It is this latter aspect of synthetic biology which makes it an attractive area for basic scientists who are trying to understand the complexity of biological organisms. Instead of the traditional molecular biology focus on studying just one single gene and its function, synthetic biology is engineering biological composites that consist of multiple genes and regulatory elements of each gene. This enables scientists to interrogate the interactions of these genes, their regulatory elements and the proteins encoded by the genes with each other. Synthesis serves as a path to analysis. One goal of synthetic biologists is to create complex circuits in cells to facilitate biocomputing, building biological computers that are as powerful or even more powerful that traditional computers. While such gene circuits and cells that have been engineered have some degree of memory and computing power, they are no match for the comparatively gigantic computing power of even small digital computers. Nevertheless, we have to keep in mind that the field is very young and advances are progressing at a rapid pace. One of the major recent advances in synthetic biology occurred in 2013 when an MIT research team led by Rahul Sarpeshkar and Timothy Lu at MIT created analog computing circuits in cells. Most synthetic biology groups that engineer gene circuits in cells to create biological computers have taken their cues from contemporary computer technology. Nearly all of the computers we use are digital computers, which process data using discrete values such as 0's and 1's. Analog data processing on the other hand uses a continuous range of values instead of 0's and 1's. Digital computers have supplanted analog computing in nearly all areas of life because they are easy to program, highly efficient and process analog signals by converting them into digital data. Nature, on the other hand, processes data and information using both analog and digital approaches. Some biological states are indeed discrete, such as heart cells which are electrically depolarized and then repolarized in periodical intervals in order to keep the heart beating. Such discrete states of cells (polarized / depolarized) can be modeled using the ON and OFF states in the biological circuit described earlier. However, many biological processes, such as inflammation, occur on a continuous scale. Cells do not just exist in uninflamed and inflamed states; instead there is a continuum of inflammation from minimal inflammatory activation of cells to massive inflammation. Environmental signals that are critical for cell behavior such as temperature, tension or shear stress occur on a continuous scale and there is little evidence to indicate that cells convert these analog signals into digital data. Most of the attempts to create synthetic gene circuits and study information processing in cells have been based on a digital computing paradigm. Sarpeshkar and Lu instead wondered whether one could construct analog computation circuits and take advantage of the analog information processing systems that may be intrinsic to cells. The researchers created an analog synthetic gene circuit using only three proteins that regulate gene expression and the fluorescent protein mCherry as a read-out. This synthetic circuit was able to perform additions or ratiometric calculations in which the cumulative fluorescence of the mCherry was either the sum or the ratio of selected chemical input concentrations. Constructing a digital circuit with similar computational power would have required a much larger number of components.  The design of analog gene circuits represents a major turning point in synthetic biology and will likely spark a wave of new research which combines analog and digital computing when trying to engineer biological computers. In our day-to-day lives, analog computers have become more-or-less obsolete. However, the recent call for unconventional computing research by the US Defense Advanced Research Projects Agency (DARPA) is seen by some as one indicator of a possible paradigm shift towards re-examining the value of analog computing. If other synthetic biology groups can replicate the work of Sarpeshkar and Lu and construct even more powerful analog or analog-digital hybrid circuits, then the renaissance of analog computing could be driven by biology.  It is difficult to make any predictions regarding the construction of biological computing machines which rival or surpass the computing power of contemporary digital computers. What we can say is that synthetic biology is becoming one of the most exciting areas of research that will provide amazing insights into the complexity of biological systems and may provide a path to revolutionize biotechnology..."


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NCBO BioPortal

NCBO BioPortal | Modern Life Science: of computers and men | Scoop.it



BioPortal, the world’s most comprehensive repository of biomedical ontologies.

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Last Release: 4.27 (May 2016) - 515 ontologies
The National Center for Biomedical Ontology is one of the National Centers for Biomedical Computing supported by the NHGRI, the NHLBI, and the NIH Common Fund
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Sandrine Palcy's curator insight, May 18, 10:18 AM
Last Release: 4.27 (May 2016) - 515 ontologies
The National Center for Biomedical Ontology is one of the National Centers for Biomedical Computing supported by the NHGRI, the NHLBI, and the NIH Common Fund
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RULBI

RULBI | Modern Life Science: of computers and men | Scoop.it
"Le Réseau des Utilisateurs de Logiciels de BioInformatique (RULBI) est depuis 2009 à l’interface entre les biologistes et les éditeurs de logiciels."
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Enquête sur les besoins en logiciels de bioinformatique des laboratoires académiques réalisée par le RULBI sous l’égide d’Aviesan, Inserm, INSB, INRA (http://goo.gl/forms/7qkQzSCbKi)
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Stemformatics - Dataset Search

Stemformatics - Dataset Search | Modern Life Science: of computers and men | Scoop.it
Datasets from 294 public studies with 4774 human and 1616 mouse samples
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"Stemformatics is not a substitute for good collaboration between bioinformaticians and stem cell biologists. We think of it as a stepping stone towards that collaboration."
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Sandrine Palcy's curator insight, April 15, 10:51 AM
"Stemformatics is a collaboration between the stem cell and bioinformatics community."
Samuel Viana's curator insight, April 15, 12:53 PM
As células tronco (em inglês, "stem cells") são muito importantes em biologia do desenvolvimento e na medicina restituitiva uma vez que são capazes de se diferenciar em qualquer tipo de célula no organismo. Num futuro não muito distante, seria possível produzir qualquer tipo de órgão em laboratório o que evitaria o eterno problema de encontrar um dador compatível aquando dos transplantes.
Este portal pretende ser uma porta de entrada para muitos estudos na área, integrando diversas bases de dados provenientes de estudos em feitos em humanos e ratos.
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Workflow4Metabolomics 2.0 | workflow4metabolomics.org

Workflow4Metabolomics 2.0 | workflow4metabolomics.org | Modern Life Science: of computers and men | Scoop.it
Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics, http://dx.doi.org/10.1093/bioinformatics/btu813
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"In addition to the Workflow4Metabolomics infrastructure for workflow management (in collaboration with IFB http://www.france-bioinformatique.fr/), MetaboHUB (http://www.metabohub.fr) has developed three additional online platforms which provide pivotal complementary functionalities for pathway metabolic network (MetExplore), spectra annotation and metabolite identification (PeakForest), and 1H-NMR spectra processing (NMRProcFlow)."
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All 2.3 Million Species Are Mapped into a Single Circle of Life

All 2.3 Million Species Are Mapped into a Single Circle of Life | Modern Life Science: of computers and men | Scoop.it
Lineages of all known species on Earth are finally pieced together
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"Researchers from a dozen institutions recently completed a three-year effort to combine tens of thousands of trees into one diagram, most readable as a circle " (Database OpenTreeOfLife.org -http://www.opentreeoflife.org/)
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Sandrine Palcy's curator insight, March 9, 6:49 AM
"Researchers from a dozen institutions recently completed a three-year effort to combine tens of thousands of trees into one diagram, most readable as a circle " (Database OpenTreeOfLife.org -http://www.opentreeoflife.org/)
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Giants in genomics: Janet Thornton

Giants in genomics: Janet Thornton | Modern Life Science: of computers and men | Scoop.it

Since October 2001, Professor Dame Janet Thornton has been director of the European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI), which shares the Wellcome Trust Genome Campus with the Wellcome Trust Sanger Institute.

Janet coordinated the ELIXIR preparatory phase (2006 – 2013) and leads the commission-funded BioMedBridges project, which clusters the biomolecular sciences research infrastructures to provide data bridges and ensure data interoperability between them. (https://erc.europa.eu/about-erc/organisation-and-working-groups/thornton-janet)



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Bio.tools : A portal to bioinformatics resources world-wide

Bio.tools : A portal to bioinformatics resources world-wide | Modern Life Science: of computers and men | Scoop.it

The Tools & Data Services Registry provides essential scientific and technical information about analytical tools and data services for bioinformatics. The registry is provided by a community effort coordinated by the Danish node of ELIXIR - the European infrastructure for biological information.

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Sandrine Palcy's curator insight, March 2, 5:22 AM
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The value and impact of the European Bioinformatics Institute (EMBL-EBI) | independent evaluation

The value and impact of the European Bioinformatics Institute (EMBL-EBI) | independent evaluation | Modern Life Science: of computers and men | Scoop.it
What is open data worth? An independent analysis of EMBL-EBI provides fascinating insights.
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An independent analysis of the value and impact of the European Bioinformatics Institute published by Charles Beagrie, Ltd. shows that for every £1 million invested, EMBL-EBI returns ~£20 million in value to the global scientific community

 

The executive summary and the full report are available online in printable format, at http://www.beagrie.com/EBI-impact-summary.pdf ; and http://www.beagrie.com/EBI-impact-report.pdf ;

 

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Biomedical sciences research infrastructures | BioMedBridges

Biomedical sciences research infrastructures | BioMedBridges | Modern Life Science: of computers and men | Scoop.it
Building data bridges from biology to medicine in Europe

BioMedBridges is a joint effort of twelve biomedical sciences research infrastructures on the ESFRI roadmap. (link is external) Together, the project partners develop the shared e-infrastructure—the technical bridges—to allow data integration in the biological, medical, translational and clinical domains and thus strengthen biomedical resources in Europe.

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Computational Microbiology and Microbiome-Based Medicine | Lipari School on Computational Life Sciences

Computational Microbiology and Microbiome-Based Medicine | Lipari School on Computational Life Sciences | Modern Life Science: of computers and men | Scoop.it
July 17 - July 24, 2016
Lipari Island, Italy

Aim and scope:
Recent advances in high-throughput sequencing and innovative tools for analyzing metagenomic data are causing a fast evolution of Computational Microbiology and Microbiome-Based Medicine. Topics such as Metatranscriptomics, Bacteria Tracking, Genome Editing, Immune System Analysis, Microbiome Analysis, Reverse Vaccinology are rising intriguing and complex questions. Our main and special guest lectures will address the scope focusing on algorithms, models, biomedical and biotechnological techniques and their clinical applications. From the enclosed bibliography, it appears that the selected themes have received much attention in the scholarly literature ranging from Nature and Science to Bioinformatics Journals.

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Program insight

Michael Levitt (Nobel Prize 2013) Stanford University, USA

 

Soren Brunak
Metatranscriptomics and transcriptional interdependencies
Novo Nordisk Foundation Center for Protein Research at University of Copenhagen and Center for Biological Sequence Analysis, Technical University of Denmark


Gene Myers
DNA Sequencing and Bacteria Tracking Systems
Max Planck Institute, Dresden, Germany



Andrea Ventura
CRISPR and somatic genome editing for cancer research
Memorial Sloan Kettering Cancer Center, New York, USA

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Rise and Demise of Bioinformatics? Promise and Progress

Rise and Demise of Bioinformatics? Promise and Progress | Modern Life Science: of computers and men | Scoop.it
The field of bioinformatics and computational biology has gone through a number of transformations during the past 15 years, establishing itself as a key component of new biology. This spectacular growth has been challenged by a number of disruptive changes in science and technology. Despite the apparent fatigue of the linguistic use of the term itself, bioinformatics has grown perhaps to a point beyond recognition. We explore both historical aspects and future trends and argue that as the field expands, key questions remain unanswered and acquire new meaning while at the same time the range of applications is widening to cover an ever increasing number of biological disciplines. These trends appear to be pointing to a redefinition of certain objectives, milestones, and possibly the field itself.
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Author: Christos A. Ouzounis Published: April 26, 2012DOI: 10.1371/journal.pcbi.1002487
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artich.io

artich.io | Modern Life Science: of computers and men | Scoop.it

artichio is a modern tool designed to ease scientific collaboration and promote Open Science & Open Data in life sciences research.

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Coming soon...

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CORBEL | sharing Services for Life-science

CORBEL | sharing Services for Life-science | Modern Life Science: of computers and men | Scoop.it

CORBEL is an initiative of eleven new biological and medical research infrastructures (BMS RIs), which together will create a platform for harmonised user access to biological and medical technologies, biological samples and data services required by cutting-edge biomedical research. CORBEL will boost the efficiency, productivity and impact of European biomedical research.

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A major Horizon 2020 project coordinated by ELIXIR (Distributed Infrastructure for life-science information - https://www.elixir-europe.org ):

"Through a user-led approach CORBEL will develop the tools, services and data management required by cutting-edge European research projects: collectively the BMS RIs will establish a sustained foundation of collaborative scientific services for biomedical research in Europe and embed the combined infrastructure capabilities into the scientific workflow of advanced users." (http://www.corbel-project.eu/about-corbel.html)

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Eterna - Invent Medicine | a serious web-based video game

Eterna - Invent Medicine | a serious web-based video game | Modern Life Science: of computers and men | Scoop.it
"Researchers at the Stanford University School of Medicine are releasing a new version of a web-based video game that will harness the creative brain power of thousands of nonscientist players."
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"The goal in coming months is for Eterna Medicine players to design a molecule that could help spur the development of a new tuberculosis test.
Tuberculosis infects a third of the world's population and kills about 1.5 million each year. Yet health organizations lack a simple-to-use blood test that can detect active infection in many patients, especially in remote villages.
Like a previous iteration of the Eterna game, the new version challenges players to build molecules of RNA with increasingly difficult-to-design shapes. " see article - http://phys.org/news/2016-05-video-game-tuberculosis.html
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DNAdigest: Empowering efficient access and sharing of Data.

DNAdigest: Empowering efficient access and sharing of Data. | Modern Life Science: of computers and men | Scoop.it
We do everything for the benefit of patients. We are a non-profit organisation empowering efficient access and sharing of genomics data.
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"DNAdigest is a charity working to promote efficient sharing of human genomic data to improve the outcome of genomic research and diagnostics for the benefit of patients. Repositive, a social enterprise spin-out of DNAdigest, is building an online platform that indexes genomic data stored in repositories and thus enables researchers to search for and access a range of human genomic data sources through a single, easy-to-use interface, free of charge."  http://dx.doi.org/10.1371/journal.pbio.1002418 ;
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Sandrine Palcy's curator insight, April 18, 11:02 AM
"DNAdigest is a charity working to promote efficient sharing of human genomic data to improve the outcome of genomic research and diagnostics for the benefit of patients. Repositive, a social enterprise spin-out of DNAdigest, is building an online platform that indexes genomic data stored in repositories and thus enables researchers to search for and access a range of human genomic data sources through a single, easy-to-use interface, free of charge."  http://dx.doi.org/10.1371/journal.pbio.1002418
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Home - OncoTrack

Home - OncoTrack | Modern Life Science: of computers and men | Scoop.it
OncoTrack, an international consortium of over 60 scientists, managed by Bayer HealthCare Pharmaceuticals and the Max Planck Institute for Molecular Genetics, has launched one of Europe’s largest collaborative academic-industry research projects to develop and assess novel approaches for identification of new markers for colon cancer.
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 "The goal of OncoTrack is to identify and characterize biological markers that will help our understanding of the variable make-up of tumours and how this affects the way patients respond to treatment. "
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GRIOTE | Groupement de Recherche en Intégration de données Omics à Très grande Echelle

GRIOTE | Groupement de Recherche en Intégration de données Omics à Très grande Echelle | Modern Life Science: of computers and men | Scoop.it
"Communauté des chercheurs en bioinformatique des Pays de la Loire autour de la thématique de l’intégration des données biologiques à très grande échelle."
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"Le Groupement de Recherche en Intégration de données Omics à Très grande Echelle est un projet fédérateur de la bioinformatique en région Pays de la Loire."
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Natural History Collections in the 21st Century | Natural museum are the original bioinformatics facilities

Natural History Collections in the 21st Century | Natural museum are the original bioinformatics facilities | Modern Life Science: of computers and men | Scoop.it

"Natural museums are the original bioinformatics facilities, exactly like the massive international online gene and protein databases that over the past 25 years have revolutionized the life sciences."

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In this inspiring article, Dr. Herman Mays, an evolutionary biologist, takes us through a journey from the 19th century natural history collections to the modern computerized biology of the 21th century.
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Tackling Big Data Generation and Usage | GEN Magazine

Tackling Big Data Generation and Usage | GEN Magazine | Modern Life Science: of computers and men | Scoop.it

"Lack of consistent metadata and semantic mapping complicates the integration of data from different sources"

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A workflow for omic data analysis - OMICtools

A workflow for omic data analysis - OMICtools | Modern Life Science: of computers and men | Scoop.it
OMICtools is a workflow for genomic, transcriptomic, proteomic, and metabolomic data analysis. All tools have been classified by omic technologies ( NGS, microarray, PCR, MS, NMR ), applications and analytical steps.
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Open PHACTS

Open PHACTS | Modern Life Science: of computers and men | Scoop.it
Bringing together pharmacological data resources in an integrated, interoperable infrastructure
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"The Open PHACTS Discovery Platform has been developed to reduce barriers to drug discovery in industry, academia and for small businesses. "

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Second Sight The Argus® II Retinal Prosthesis System

Second Sight The Argus® II Retinal Prosthesis System | Modern Life Science: of computers and men | Scoop.it
The Argus II Retinal Prosthesis System ("Argus II") is the world's first approved device intended to restore some functional vision for people suffering from blindness. Argus II is approved for use in the United States and the European Economic Area.
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When computers give data back to humans

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SciBite : Text Mining, Competitor Intelligence and Semantics

SciBite : Text Mining, Competitor Intelligence and Semantics | Modern Life Science: of computers and men | Scoop.it

SciBite is a new informatics company, set up to provide access to drug discovery intelligence data to all, from non-profits to large pharma. We use a unique text-mining system to monitor the entire internet for drug intelligence data, combining this with expert curated dictionaries covering a broad range of drug discovery topics.

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TailorDev

TailorDev | Modern Life Science: of computers and men | Scoop.it

TailorDev is a french startup based in Clermont-Ferrand (Auvergne). Our mission is to develop modern tools to ease scientific collaboration and promote Open Science & Open Data in life sciences research.

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TailorDev has developped artich.io, a collaborative solution for life scientists, which will be soon available (more @ https://artich.io/).

 

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Sandrine Palcy's curator insight, December 3, 2015 7:04 AM

TailorDev has developped artich.io, a collaborative solution for life scientists, which will be soon available (more @ https://artich.io/).

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eTRIKS | building a sustainable IMI translational research informatics/Knowledge Management platform

eTRIKS | building a sustainable IMI translational research informatics/Knowledge Management  platform | Modern Life Science: of computers and men | Scoop.it

eTRIKS is the result of a collaboration between 17 different partners. Each combining their strenghts in the development of a platform and services for data staging, exploration and use in translational research.

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"The Innovative Medicines Initiative (IMI) is Europe's largest public-private initiative aiming to speed up the development of better and safer medicines for patients." http://www.imi.europa.eu/

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