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Bioinformatics, blended with education and health sciences subjects
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Free Download Computational Nanotechnology - Modeling and ...

Free Download Computational Nanotechnology - Modeling and ... | Bioinformatics Training | Scoop.it
Home > Free Download Computational Nanotechnology - Modeling and Applications with MATLAB , Free Download Free Downloads - DownTR > Free Download Computational Nanotechnology - Modeling and Applications ...
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Biofuel waste product recycled for electricity | Science Codex

Biofuel waste product recycled for electricity | Science Codex | Bioinformatics Training | Scoop.it
A by-product of biofuel manufacture can power microbial fuel cells to generate electricity cheaply and efficiently, according to scientists presenting their work at the Society for General Microbiology's Autumn Conference.
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Digital Data Storage in DNA | Bio 2.0 | Learn Science at Scitable

Digital Data Storage in DNA | Bio 2.0 | Learn Science at Scitable | Bioinformatics Training | Scoop.it

by

Eric Sawyer

"In today's world of high technology, we usually associate digital information with computers, satellites, and smart phones. But don't forget that digital information storage far predates the digital age. When Watson and Crick discovered the structure of DNA, they also discovered that at the heart of living things is a massive digital information storage molecule. The digital information in the human genome encodes the instructions for building the human body that would ultimately go on to build digital computers.

Bringing this full circle, a recent paper1 explores the possibility of using synthetic DNA to store digital information of human design. We have a data problem. The future of science seems to be big data, and that's challenging and expensive to store. The CMS experiment at the Large Hadron Collider alone generates 1 terabyte of data every second and, more poetically, in its projected lifetime the LHC will give us a dataset comparable in size to a library containing every single word spoken by every human who has ever lived2. Big science aside, the internet and social media generate large quantities of digital information.

In their paper, George Church and colleagues combine recent advances in DNA synthesis and sequencing to create a data storage chip made of DNA. In the DNA chip they stored a HTML file of a synthetic biology book, containing 53,426 words of text, 11 black and white JPEG images, and a computer program written in Java. Since DNA contains four bases, two computer bits can be encoded per DNA base: e.g., A = 00, C = 01, G = 10, T = 11. The authors of this paper however decided to use a one base per bit code, A = 0, C = 0, G = 1, T = 1, which allows for many synonymous encodings to avoid sequences that are difficult to sequence such as long repeats.

In all, they synthesized 54,898 short pieces of DNA. Each contained 2 primer binding sites for PCR amplification and sequencing, a unique 19-base address, and 96 bases (96 bits, or 12 bytes) of stored data (see the figure). Their DNA chip represents the densest information storage (nearly 1016 bits/mm3) to date, beating the likes of in vivo experiments, flash memory, hard disks, and CDs. The error rate was an impressively low 10 bits out of the total 5.27 million.

The prospect of storing something like particle accelerator data on a synthetic DNA chip is intriguing and seductively poetic, but I'm a bit skeptical. The interface between computer chips and DNA chips will never be as seamless as the interface between computer chips and hard disks, flash memory storage devices, etc. And even though DNA sequencing is getting much cheaper, and even more portable, it seems unlikely that individuals would purchase sequencers. But maybe DNA will be used for long-term archiving as the authors suggest, where the need for high capacity, high longevity storage outweighs the costly and time-consuming process of writing and reading the stored data."

http://bit.ly/NP6E3y


Via Gerd Moe-Behrens
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katielouisemilburn's curator insight, March 14, 2013 6:43 AM

phones are cool i take my everywhere and my i pad totally cool are you?

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Handbook of Theoretical and Computational Nanotechnology

Handbook of Theoretical and Computational Nanotechnology | Bioinformatics Training | Scoop.it
Handbook of Theoretical and Computational Nanotechnology.

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5 Ways Classrooms Can Learn From Mobile Apps via @joevans

5 Ways Classrooms Can Learn From Mobile Apps via @joevans | Bioinformatics Training | Scoop.it
Mobile phones have historically been banned from the classroom and seen as a distraction to education. But with new developments in education apps, there are some…...

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The Computational Life: Is your prof getting laid? Part 1: The Markov Model

The Computational Life: Is your prof getting laid? Part 1: The Markov Model | Bioinformatics Training | Scoop.it

What the heck is a Markov model?

Markov models pervade computational biology, so I think they provide a good starting point for a computational biology blog. The fundamentals of these models were originally deduced by Andrey Markov, a man who - like many other great thinkers - managed to get himself excommunicated from a large religious institution. Though, unlike the others, his banishment was by choice.Markov models have many uses across a wide range of disciplines. I primarily use them to model how nucleotides or amino acids change over evolutionary time or how these biological sequences change over space. Speech processing specialists use them to model sounds in words; linguists use them to model grammars; and social scientists use them to model whatever the hell those guys do. The point is that if you are interested in describing/simulating/performing inference on some phenomenon that takes on discrete states (or something that can be turned into discrete states), a Markov model can prove quite useful.

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A Curated Selection of Data Visualization Charts and Infographics: The Information Is Beautiful Awards

A Curated Selection of Data Visualization Charts and Infographics: The Information Is Beautiful Awards | Bioinformatics Training | Scoop.it

Robin Good: David McCandlees, the author of the book Information is Beautiful celebrates great data visualization and information design work through the Information is Beautiful Awards.

Together with a jury of experts like Brian Eno, Paola Antonelli, Maria Popova, Simon Rogers and Aziz Kami, he has curated a unique selection of 300 designs and a short list of finalists in the following categories:

 

» Data visualization– A singular visualisation of data or information.» Infographic – Using multiple data visualisations in service to a theme or story

 

» Interactive visualization – Any viz where you can dynamically filter or explore the data.

 

» Data journalism – A combination of text and visualizations in a journalistic format.

 

» Motion infographic – Moving and animated visualizations along a theme or story.

 

» Tool or website – Online tools & apps to aid datavizzing.

 

The selection itself is worth a tour of the site and of this initiative.

 

Check: http://www.informationisbeautifulawards.com/

 

Longlist selection: http://www.informationisbeautifulawards.com/2012/07/our-longlist/

 

Shortlist selection: http://www.informationisbeautifulawards.com/2012/08/awardshortlist/

 

 


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New Genitalia-Headed Fish Is Evolutionary Mystery - National Geographic

New Genitalia-Headed Fish Is Evolutionary Mystery - National Geographic | Bioinformatics Training | Scoop.it
National GeographicNew Genitalia-Headed Fish Is Evolutionary MysteryNational GeographicHow's this for a head turner? A tiny new species of fish from Vietnam sports its genitalia on its noggin.
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Will Overregulation In Europe Stymie Synthetic Biology? - Forbes

Will Overregulation In Europe Stymie Synthetic Biology? - Forbes | Bioinformatics Training | Scoop.it
In any one of several fields of endeavor, synthetic biology could lead to technology’s Next Big Thing.

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Genome Brings Ancient Girl to Life - ScienceNOW

Genome Brings Ancient Girl to Life - ScienceNOW | Bioinformatics Training | Scoop.it
Genome Brings Ancient Girl to Life - ScienceNOW...
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ViewPoint 3D - create stunning 3D presentations

ViewPoint 3D - create stunning 3D presentations | Bioinformatics Training | Scoop.it
ViewPoint 3D is the next generation of presentation software, adding a third dimension to your presentations.

ViewPoint3D is completely free for educational use.


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Totally Addictive Education: The Future of Learning - Forbes

Totally Addictive Education: The Future of Learning - Forbes | Bioinformatics Training | Scoop.it
Today, most educational systems are designed to work from the microscopic to the macroscopic. Students learn facts and figures and tiny fractions of knowledge long before anyone really puts things into a larger context.
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Electronic Health Records In the Classroom? | The Health Care Blog

Electronic Health Records In the Classroom? | The Health Care Blog | Bioinformatics Training | Scoop.it
RT @THCBstaff: The Health Care Blog | Electronic Health Records In the Classroom?

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Intro

Intro | Bioinformatics Training | Scoop.it

Synthetic Biology: A new 'Age of Wonder'?

Synthetic Biology approaches are catalysing a paradigm shift in genetic manipulation and the engineering of biology. Liberated by rapid, reliable methods for DNA synthesis and assembly, researchers are now able to routinely build synthetic circuits well beyond the scale and complexity of the single gene insertions that characterise the genetically engineered systems of the last forty years. Established design principles, facile assembly from standardised parts and predictable performance have long been the defining features of modern engineering and represent the core goals of Synthetic Biology. Of these, rational and reliable design remains the most challenging problem faced by the synthetic biologist.

On Tuesday 25th September, the University of Cambridge’s Centre for Mathematical Sciences plays host to the first Cambridge BioDesign TechEvent. The TechEvent will bring together researchers from around Cambridge, the UK and beyond, strengthening existing relationships and building new ones, while focusing in detail on research and development in the field of Synthetic Biology. The day provides a platform for experts in the field to present the latest developments in bioengineering, providing insight into the cutting edge technologies set to define the 21st Century.

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Academic Libraries: Neanderthals In Open Access Evolution? | Science Codex

Academic Libraries: Neanderthals In Open Access Evolution? | Science Codex | Bioinformatics Training | Scoop.it
In April, academic and professional publisher SAGE convened a roundtable in association with the British Library to discuss the role of the academic library in an open access (OA) future - namely, how to stay relevant.
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The value of data : Nature Genetics : Nature Publishing Group

The value of data : Nature Genetics : Nature Publishing Group | Bioinformatics Training | Scoop.it

Data citation and the derivation of semantic constructs directly from datasets have now both found their place in scientific communication. The social challenge facing us is to maintain the value of traditional narrative publications and their relationship to the datasets they report upon while at the same time developing appropriate metrics for citation of data and data constructs.

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How to Participate in a Nearpod Presentation on the Web

How to Participate in a Nearpod Presentation on the Web | Bioinformatics Training | Scoop.it
Learn how students can participate on Nearpod presentations through the Student web app, available on the School Edition.

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The Computational Life: Is your prof getting laid? Part 2: The stationary distribution

The Computational Life: Is your prof getting laid? Part 2: The stationary distribution | Bioinformatics Training | Scoop.it

Part 2: The stationary distribution

To recap

As I began here, there is a professor whose love life has an impact on how she interacts with the class. Eventually, I will get into how to mathematically deduce her relationship status given her interactions with the class. For now, I'm focusing on how to model the relationships themselves.

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A visualization of Gold Open Access options - Ross Mounce

A visualization of Gold Open Access options - Ross Mounce | Bioinformatics Training | Scoop.it
To try and publicize the variety of Gold Open Access article publication options on offer, I’ve decided to create a visualization of the journal data that has previously been collected as part of my survey of ‘Open Access’ publisher licenses’ spreadsheet.
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Nanomedicine Will Destroy Antibiotic-Resistant Bacteria

Nanomedicine Will Destroy Antibiotic-Resistant Bacteria | Bioinformatics Training | Scoop.it
Humans have made the regrettable mistake of overusing both antibiotics and antimicrobial consumer products.

Via Cedric Louis, Luís Bastos
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Schedule for the 2012 Bioinformatics Short Course on Next ...

Schedule for the 2012 Bioinformatics Short Course on Next ... | Bioinformatics Training | Scoop.it
The schedule for our week-long bioinformatics training course: the 2012 Bioinformatics Short Course on Next-Generation Sequencing is now live. The course is an intense 5-day training workshop for bioinformaticians both novice and ...
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Frontiers | Cell-to-cell communication circuits: quantitative analysis of synthetic logic gates | Frontiers in Systems Physiology

Frontiers | Cell-to-cell communication circuits: quantitative analysis of synthetic logic gates | Frontiers in Systems Physiology | Bioinformatics Training | Scoop.it

by

Hoffman-Sommer M, Supady A, Klipp E.

"One of the goals in the field of synthetic biology is the construction of cellular computation devices that could function in a manner similar to electronic circuits. To this end, attempts are made to create biological systems that function as logic gates. In this work we present a theoretical quantitative analysis of a synthetic cellular logic-gates system, which has been implemented in cells of the yeast Saccharomyces cerevisiae (Regot et al., 2011). It exploits endogenous MAP kinase signaling pathways. The novelty of the system lies in the compartmentalization of the circuit where all basic logic gates are implemented in independent single cells that can then be cultured together to perform complex logic functions. We have constructed kinetic models of the multicellular IDENTITY, NOT, OR, and IMPLIES logic gates, using both deterministic and stochastic frameworks. All necessary model parameters are taken from literature or estimated based on published kinetic data, in such a way that the resulting models correctly capture important dynamic features of the included mitogen-activated protein kinase pathways. We analyze the models in terms of parameter sensitivity and we discuss possible ways of optimizing the system, e.g., by tuning the culture density. We apply a stochastic modeling approach, which simulates the behavior of whole populations of cells and allows us to investigate the noise generated in the system; we find that the gene expression units are the major sources of noise. Finally, the model is used for the design of system modifications: we show how the current system could be transformed to operate on three discrete values."
http://bit.ly/TGfy66


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UC Davis students work to engineer plastic-degrading bacteria - The Sacramento Bee

UC Davis students work to engineer plastic-degrading bacteria - The Sacramento Bee | Bioinformatics Training | Scoop.it
Every weekday this summer, 10 students from different departments at UC Davis have come together in the university's Genome Center to work on what they hope will one day be the answer to cleaning up the world's landfills.
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New Grant and Governance Structure Will Help Support arXiv - Wired Campus - The Chronicle of Higher Education

New Grant and Governance Structure Will Help Support arXiv - Wired Campus - The Chronicle of Higher Education | Bioinformatics Training | Scoop.it

The Simons Foundation has awarded Cornell a five-year operating grant to match the fees it gets from arXiv’s member institutions, up to $300,000 a year. And this fall those institutions will elect a member advisory board to help govern the repository. Those steps build off the voluntary membership model Cornell introduced in January 2010, saying it needed to find ways to share the costs of maintaining the repository.

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Academic Librarian Research: A Survey of Attitudes, Involvement, and Perceived Capabilities

Academic Librarian Research: A Survey of Attitudes, Involvement, and Perceived Capabilities | Bioinformatics Training | Scoop.it

One of the interesting articles in the latest issue of College & Research Libraries (September 2012) is this article on the development and results of a recent survey of academic librarians about their attitudes, involvement, and perceived capabilities using and engaging in primary research. The purpose of the survey was to inform the development of a continuing education program in research design.

 

"This article contributes a new perspective on the topic of how librarians think of their own abilities to conduct research with the introduction of a confidence scale and opens a line of inquiry for possible future research activities related to self-efficacy and research productivity..."


"Two other potentially profitable research agendas are identified in this article: defining a research culture in a library setting and performing a systematic review of published academic librarian practitioner-researchers to learn how to replicate their success."

 

The article (as well as all the articles in this issue) are available for download in pdf and html here: http://crl.acrl.org/content/73/5/431.full.pdf+html


Via Fe Angela M. Verzosa
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