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3quarksdaily: Synthetic Biology: Engineering Life To Examine It

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

Via Socrates Logos, Pedro Fernandes
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From computing biology to biology for computing...!

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Socrates Logos's curator insight, January 7, 2:33 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..."


 http://bit.ly/19Ywxwn

Modern Biology: of computers and men
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MolMeth

MolMeth | Modern Biology: of computers and men | Scoop.it

MolMeth is a crowd reviewed platform to disseminate protocols and SOP:s. Anyone can rate protocols and registered users can also provide signed reviews or comments.

Sandrine Palcy's insight:

The Molecular Methods database (MolMeth) is a structured database intended to provide researchers with an efficient resource to create, develop and publish life science laboratory protocols.

The Molecular Methods database is funded by BBMRI.se and hosted by the SLU Global Bioinformatics Centre in Uppsala, Sweden.

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Human Proteome Mapped | The Scientist Magazine®

Human Proteome Mapped | The Scientist Magazine® | Modern Biology: of computers and men | Scoop.it
Compiling mass spectrometry profiles of human tissues and cell lines, two separate groups publish near-complete drafts of the human proteome.
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The robot that moves like a human | Horizon Magazine - European Commission

The robot that moves like a human | Horizon Magazine - European Commission | Modern Biology: of computers and men | Scoop.it
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The principles behind the EU-funded ECCERobot project could be used to inspire future robots that are designed to work around people.

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eLife | The open-access journal for outstanding advances in life science and biomedicine, backed by the funders of research

eLife | The open-access journal for outstanding advances in life science and biomedicine, backed by the funders of research | Modern Biology: of computers and men | Scoop.it
Sandrine Palcy's insight:

eLife Sciences is a unique, non-profit collaboration between the funders and practitioners of research to improve the way important results are presented and shared. The open-access eLife journal is the first step in this initiative to make science publishing more effectively benefit science and scientists.

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The End of Insight: Will Computers Replace Scientists?

The End of Insight: Will Computers Replace Scientists? | Modern Biology: of computers and men | Scoop.it
Can robots work as scientists? At first, this seems like a silly question.
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"Of computers and men"...Well, for how long...?

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France latest country to join ELIXIR | ELIXIR

France latest country to join ELIXIR | ELIXIR | Modern Biology: of computers and men | Scoop.it
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At last....!

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HUPO-PSI - HUPO Proteomics Standards Initiative

HUPO-PSI - HUPO Proteomics Standards Initiative | Modern Biology: of computers and men | Scoop.it

The HUPO Proteomics Standards Inititative defines community standards for data representation in proteomics to facilitate data comparison, exchange and verification.

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Life Science Technologies: Biology Watches the Cloud

Life Science Technologies: Biology Watches the Cloud | Modern Biology: of computers and men | Scoop.it
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When biology becomes cloudy...

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A Cell Biologist's Guide to Modeling and Bioinformatics PDF EBook Download - а.галехбан

A Cell Biologist's Guide to Modeling and Bioinformatics PDF EBook Download - а.галехбан | Modern Biology: of computers and men | Scoop.it
A Cell Biologist's Guide to Modeling and Bioinformatics PDF (A Cell Biologist’s Guide to Modeling and Bioinformatics PDF EBook Download http://t.co/sD25sVkUYl)...
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L’analyse de données RNA-seq: mode d’emploi | bioinfo-fr.net

L’analyse de données RNA-seq: mode d’emploi | bioinfo-fr.net | Modern Biology: of computers and men | Scoop.it
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What is the CHPP Project?

What is the CHPP Project? | Modern Biology: of computers and men | Scoop.it

Our rationale is that effective integration of proteomics data into a genomic framework will lead to improved knowledge of complex biological systems and facilitate access to protein level data (Paik YK. et. al., Nat Biotechnology, 30(3), 221-223, 2012).

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Nature ENCODE : Nature Publishing Group : A landmark in the understanding of the human genome

Nature ENCODE : Nature Publishing Group : A landmark in the understanding of the human genome | Modern Biology: of computers and men | Scoop.it
Nature ENCODE: Explore the wealth of information about the project's key findings and numerous integrative analyses.
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Welcome to the Nature ENCODE site. Here you will find the overview ENCODE paper in which the consortium describes the project’s key findings and numerous integrative analyses.

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An analysis of a ‘community-driven’ reconstruction of the human metabolic network - Springer

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Review of human metabolic network Recon 2: a knowledgebase and a predictive model.

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EpiC: Antigenicity And Functional Prediction

EpiC: Antigenicity And Functional Prediction | Modern Biology: of computers and men | Scoop.it
EpiC, a tool to aid researchers in the selection of epitope
for affinity proteomics. Meta-server for prediction of antigenicity.
Sandrine Palcy's insight:

EpiC collates and presents a structure-function summary and antigenicity prediction of your protein to help you design antibodies that are appropriate to your planned experiments.

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GOBLET | Global Organisation for Bioinformatics Learning, Education & Training

GOBLET | Global Organisation for Bioinformatics Learning, Education & Training | Modern Biology: of computers and men | Scoop.it
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A global umbrella to coordinate and foster bioinformatics knowledge diffusion.

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Organic circuits - lighter, cheaper and bendier | Horizon Magazine - European Commission

Organic circuits - lighter, cheaper and bendier | Horizon Magazine - European Commission | Modern Biology: of computers and men | Scoop.it
European scientists are developing flexible alternatives to silicon.
Sandrine Palcy's insight:

A new type of plastic electronics made from organic materials is lighter, cheaper, and more flexible than any of today’s technology. Such circuits could be worn on clothing or placed inside medical sensors.

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3quarksdaily: Synthetic Biology: Engineering Life To Examine It

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

Via Socrates Logos, Pedro Fernandes
Sandrine Palcy's insight:

From computing biology to biology for computing...!

more...
Socrates Logos's curator insight, January 7, 2:33 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..."


 http://bit.ly/19Ywxwn

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Journées succès France Grille - Mettre en place une infrastructure informatique dédiée aux sciences de la vie - 2013-11-13 (Webcast CC-IN2P3/CNRS )

Journées succès France Grille - Mettre en place une infrastructure informatique dédiée aux sciences de la vie - 2013-11-13 (Webcast CC-IN2P3/CNRS ) | Modern Biology: of computers and men | Scoop.it
Sandrine Palcy's insight:

L'Institut Français de Bioinformatique : mettre en place une infrastructure informatique dédiée aux sciences de la vie - Jean-François GIBRAT (INRA)

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BigBrain Atlas Unveiled | Science/AAAS | News

BigBrain Atlas Unveiled | Science/AAAS | News | Modern Biology: of computers and men | Scoop.it
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Access the resource here: https://bigbrain.loris.ca/main.php

 

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Trouble at the lab

Trouble at the lab | Modern Biology: of computers and men | Scoop.it
“I SEE a train wreck looming,” warned Daniel Kahneman, an eminent psychologist, in an open letter last year. The premonition concerned research on a phenomenon...
Sandrine Palcy's insight:

Let 's talk about research DATA in general ... May be there are less valuable DATA to be stored?

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BioData Mining - Unraveling genomic variation from next generation sequencing data

Elucidating the content of a DNA sequence is critical to deeper understand and decode the genetic information for any biological system.
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Chromosome Walk - Au fil du génome humain | SIB

Chromosome Walk - Au fil du génome humain | SIB | Modern Biology: of computers and men | Scoop.it

Chromosome walk: exposition virtuelle pour découvrir le génome humain, l’ADN, les gènes, les protéines et la bioinformatique /

A saunter along the human genome…take a walk and discover the world of genes, proteins and bioinformatics.

Sandrine Palcy's insight:

Bonne visite / good visit!

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deCODE

deCODE | Modern Biology: of computers and men | Scoop.it

 

In the seconds it takes after you press the above deCODE button, I will ...

Change the letters of your name to the closest DNA bases...Search every one of 168,297 protein sequences from 8826 animals, plants and microorganisms...And return to you, the protein that contains the closest match to... the letters of your name !!

 

Sandrine Palcy's insight:

COOOOL!!!

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Best practices in bioinformatics training for life scientists

Best practices in bioinformatics training for life scientists | Modern Biology: of computers and men | Scoop.it
Sandrine Palcy's insight:

" Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe."

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elixir_usersurvey_finalreport.pdf

Sandrine Palcy's insight:

A European survey of needs and priotities for bioinformatics infrastructures from users' point of view: preparatory phase of ELIXIR project.

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