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Bioinformatics Training
Bioinformatics, blended with education and health sciences subjects
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Why Curation Is Important for Education and Learning: 10 Key Reasons, Tools and Resources

Why Curation Is Important for Education and Learning: 10 Key Reasons, Tools and Resources | Bioinformatics Training | Scoop.it

Robin Good: Content curation will play a major role both in the way we "teach" and in the way we educate ourselves on any topic. When and where it will be adopted, it will deeply affect many key aspects of the educational ecosystem.

 

This article, builds up over my recent presentation on Content Curation for Education that I delivered at Emerge2012 virtual conference.

 

In that presentation I claimed that the adoption of "curation approaches" will directly affect the way competences are taught, how textbooks are put together, how students are going to learn about a subject, and more than anything, the value that can be generated for "others" through a personal learning path.

 

If we learn not by memorizing facts, but by collaborating with others in the creation of a meaningful collection-explanations of specific topics/issues/events then, for the first time in history, we can enrich planetary knowledge each time we take on a new learning task.

 

And it's already happening.

 

Yes, we are only at the very early stages, but, in my humble opinion, there are enough signs and indications that this is not going to be something marginal.

 

In this article I outline ten key factors, already at work, which, among others, will very likely pave the way for a much greater and rapid adoption of curation practices in the educational / academic world.

 

Full article: http://www.masternewmedia.org/curation-for-education-and-learning/

 

(Image credit: Shutterstock)

 

 

 


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Giuseppe Mauriello's comment, August 9, 2012 9:41 AM
Thanks Robin!
I scooped your article one hour ago! :-)
Ken Morrison's comment, August 10, 2012 4:15 AM
Thank you for the rescoop. If your aren't following him already, I highly suggest following Robin Good's topics on here. There is some great information about wise curation there. Good luck to you :)
Ken
Ken Morrison's comment, August 17, 2012 8:26 AM
Thank you for the rescoop. I appreciate your scoop.it sites. Your 4th Era one was one of the first that I began following.
Ken
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Painting with cells | Broad Institute of MIT and Harvard

Painting with cells | Broad Institute of MIT and Harvard | Bioinformatics Training | Scoop.it

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Citizen Scientists Track European Heredity | The Synthetic Bestiary – Synthetic Biology, Genetic Engineering, and The Future

Citizen Scientists Track European Heredity | The Synthetic Bestiary – Synthetic Biology, Genetic Engineering, and The Future | Bioinformatics Training | Scoop.it

Citizen scientists have recently published a paper in PLOS One tracking human male migration and expansion, using the R1b1a2 gene on the Y chromosome. What makes this work special is the citizen scientist aspect of it. Following on from our previous article on bioinformatics as a growing hobby, this work shows that such a hobby can be a truly useful form of crowd sourced science. One of the authors of the paper remarked:

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New Kenyan fossils shed light on early human evolution - EurekAlert (press release)

New Kenyan fossils shed light on early human evolution - EurekAlert (press release) | Bioinformatics Training | Scoop.it
New Kenyan fossils shed light on early human evolutionEurekAlert (press release)NAIROBI, KENYA – Exciting new fossils discovered east of Lake Turkana confirm that there were two additional species of our genus – Homo – living alongside our direct...
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Rescooped by Pedro Fernandes from Health and Biomedical Informatics
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Bioinformatics Meets User-Centred Design: A Perspective « EBI ...

We are happy to announce that EMBL-EBI's latest article on user experience in bioinformatics has just been published in the peer-reviewed open access journal, PLoS Computational Biology. We hope this article is just the ...

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Why Blood is Red!

VMD is distributed free and developed by the NIH and is one of the most widely used pieces of molecular visualisation software in the world.
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Rescooped by Pedro Fernandes from Next Gen Sequencing (NGS) and Bioinformatics at UVic
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PLoS Pathogens: Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology

PLoS Pathogens: Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology | Bioinformatics Training | Scoop.it

Whole genome sequencing (WGS) promises to be transformative for the practice of clinical microbiology, and the rapidly falling cost and turnaround time mean that this will become a viable technology in diagnostic and reference laboratories in the near future. The objective of this article is to consider at a very practical level where, in the context of a modern diagnostic microbiology laboratory, WGS might be cost-effective compared to current alternatives. We propose that molecular epidemiology performed for surveillance and outbreak investigation and genotypic antimicrobial susceptibility testing for microbes that are difficult to grow represent the most immediate areas for application of WGS, and discuss the technical and infrastructure requirements for this to be implemented.


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Marion Koopmans's curator insight, February 16, 2013 11:03 AM

Nice conceptual figures

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Upgrading Synthetic Biology's Toolkit: New Method Could Enable Reprogramming of Mammalian Cells | ZeitNews

Upgrading Synthetic Biology's Toolkit: New Method Could Enable Reprogramming of Mammalian Cells | ZeitNews | Bioinformatics Training | Scoop.it

Through the assembly of genetic components into "circuits" that perform logical operations in living cells, synthetic biologists aim to artificially empower cells to solve critical problems in medicine, energy and the environment. To succeed, however, they'll need far more reliable genetic components than the small number of "off-the-shelf" bacterial parts now available

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Big Data: the key to solving healthcare's data problems?

Big Data: the key to solving healthcare's data problems? | Bioinformatics Training | Scoop.it

Lorraine Lawson writes:

 

'Oracle recently released a report noting, among other things, that healthcare isn’t prepared to manage Big Data. That’s hardly shocking, since healthcare seems largely inept at managing any data, much less Big Data, which is generally defined as having one or more of these characteristics:

 

* Variety, meaning structured, semi-structured and unstructured data
* Velocity, meaning you want it moved at high speeds
* Volume, think petabytes and terabytes

 

Maybe health care IT doesn’t have a data problem so much as it has a Big Data problem.

 

What do I mean? Well, most health care records actually fall into the domain of Big Data more than your typical, relational database kind of data. Specifically:

 

* Most health care records are actually unstructured data, e.g., text documents or images. Doctor’s notes on patients, nurse’s care plans, lab results, x-rays and MRI results all fall well outside the domain of structured data. I


* Health care data is often high volume, particularly when you’re talking about a state or national electronic health records system. What’s more, when you deal with images, like x-rays or other scans, you’re increasing the data’s volume in terms of storage requirements.


* Finally, most health care records need to be moved relatively quickly, and as individual records. So, if I’m having a consult tomorrow with a surgeon, then the x-rays need to be at the office by morning.

 

It looks like there’s a clear use case for Big Data technologies in health care.

 

In fact, if I may be so bold, maybe health care’s data problems are not entirely caused by niche vendors, data silos and a lack of investment.

 

Maybe the reason health care IT is such a mess is because the existing tools couldn’t handle Big Data needs in an affordable way.


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Content Curation Can Help Education System Breed Future Workskills

Content Curation Can Help Education System Breed Future Workskills | Bioinformatics Training | Scoop.it

Robin Good: If you are interested in exploring content curation as a possible venue for innovating teaching and learning approaches, you will find lots of valuable information in this new article by @NancyW entitled Developing Future Workskills Through Content Curation.

 

In it she points to a study conducted last year, the Apollo Research Institute Future Workskills 2020, that identifies critical workskills needed for future jobs and how fitting "content curation" may be in cultivating and refining many of those.

 

She writes: "A closer look suggests that critical workforce skills identified in this \ study can be easily aligned with the skills practiced with content curation.


The skills a student employs to successfully curate information include curiosity, media literacy, ability to make connections across disciplines, information literacy, the ability to evaluate and understand perspective, synthesize and evaluate information, and a good dose of self-direction."

 

"Future Workskills 2020 suggests a monumental shift and change needs to begin now in our education system.

 

These skills can be developed through the process of content curation.

 

Content curation has the added benefit of helping students find their passions for and take ownership of their learning..."

 

 

Right on target. Recommended. 8/10

 

Full article: http://d20innovation.d20blogs.org/2012/07/27/developing-future-workskills-through-content-curation/

 

 


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GTPB: ARANGS12 Bioinformatics Training Course

GTPB: ARANGS12 Bioinformatics Training Course | Bioinformatics Training | Scoop.it

Course Description

 

Next generation sequencing (NGS) technologies for DNA have resulted in a yet a bigger deluge of data. Researchers are learning that analysing such data sets is becoming the bottleneck in their work. In many cases, several steps in these analyses are fairly generic (e.g. quality control filtering, alignment to reference sequences, typing) so that off-the-shelf pipelines can be applied. In other cases, novel research approaches require development of new analysis pipelines. Either way, all analysis steps should be repeatable and any changes made to the data (e.g. renaming, annotation, alignment) should be recorded so that the provenance of the results is clear and inferences are reproducible. In this brief workshop we will establish several best practices of reproducibility and provenance recording in the (comparative) analysis of data obtained by NGS. In doing so we will encounter the c ommonly used technologies that enable these best practices by working through use casesthat illustrate the underlying principles.

 

 Best practices

   Standardized project organization

   Projects fully 'runnable' without user intervention

   No loss of data, metadata or source code through versioning

 

 Technologies

     Next generation sequencing platforms

     File formats

     Command-line executables,

           command line scripting and batching

     High-level programming with domain-specific toolkits

     Revision control systemsWorkflow environments

 

  Use cases

     Phylogenetic placement of metagenomic data

     Typing of pathogens

     Comparative analysis of multicellular genomic data

 

http://gtpb.igc.gulbenkian.pt/bicourses/ARANGS12/

 

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Translational Bioinformatics: Transforming 300 Billion Points of Data

Translational Bioinformatics: Transforming 300 Billion Points of Data into Diagnostics, Therapeutics, and New Insights into Disease Air date: Wednesday, June...
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TEDxNYU - Christopher Bradley - Synthetic Biology: This Will Change Everything

by

TEDxNYU

"In this fascinating talk Christopher Bradley shows us that our world is about to change radically thanks to the promise of Synthetic Biology."

"About Christopher Bradley
Christopher is a student at NYU Poly, where he studies Computer Science and Biology, two fields that are rapidly converging. He is also the founder of Synthetic Biosystems Inc., a company working on next-generation software applications in the fields of Biotechnology, Healthcare IT, and Synthetic Biology."
http://bit.ly/LZjQ9H


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iPad As.... Different Apps for Different Activities - All in a Chart

iPad As.... Different Apps for Different Activities - All in a Chart | Bioinformatics Training | Scoop.it
EdTechTeacher provides professional development services to teachers, schools, districts, and administrators.

...


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Bioinformatics as a Hobby | The Synthetic Bestiary – Synthetic Biology, Genetic Engineering, and The Future

Bioinformatics as a Hobby | The Synthetic Bestiary – Synthetic Biology, Genetic Engineering, and The Future | Bioinformatics Training | Scoop.it

Bioinformatics is the study of data generated from biological experiments. With the advent of high-throughput sequencing and many other rapidly improving technologies Biologists are often producing far more data than they can properly analyze. With data being so easy to produce we have massive amounts of data, much of it publicly available – which could hold the keys to new medicines, cures, of breakthroughs. This data just needs someone to look through it. Using data mining software bioinformaticians look though data to find interesting patterns or to find answers to questions. But just like DIY Biology, bioinformatics isn’t restricted to professionals. Given that all you need to do bioinformatics is a computer and some spare time, anyone can do it.

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E-Learning: Confusing Terminology, Research Gaps and Inherent Challenges | Guri-Rosenblit | The Journal of Distance Education / Revue de l'Éducation à Distance

This article examines the problem of defining a broad conceptual theory for the applications of the advanced technologies in educational settings, most particularly in higher education. The article starts with discussing the multiple and confusing meanings of e-learning in the relevant literature; it proceeds to examine the problem of putting the learners in the center of the study process and exaggerating their self-directed abilities; it identifies noticeable gaps in the e-learning research; and it concludes with an analysis of some inherent challenges embedded in both conducting meaningful research on the advanced technologies in learning/teaching settings and in their actual implementation.

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Synthetic Biology Firms Ally on Infectious Disease mAbs

Synthetic Biology Firms Ally on Infectious Disease mAbs | Bioinformatics Training | Scoop.it

 

"Synthetic Biologics is giving Intrexon $3.6 million worth of its shares as part of a second exclusive collaboration, through which the firm will use Intrexon’s technologies to develop monoclonal antibodies against initially three, but potentially five, different infectious diseases. Synthetic Biologics and Intrexon’s initial collaboration is focused on the development and commercialization of a DNA-based therapeutic for the treatment of pulmonary arterial hypertension (PAH).

Under terms of the new deal Synthetic Biologics will have broad access to Intrexon’s full suite of technologies, including its core UltraVector™ platform for the design, construction, and testing of genetic components, mAbLogix™ platform for in vitro B-cell library production, Laser-enabled analysis and processing™ (LEAP™) cell processing station, and genome/protein engineering expertise. The addition of the $3.6 million worth of shares to Intrexon's existing holding in the firm will give it an 18% stake in Synthetic Biologics.

“Intrexon has state-of-the art technologies and efficient processes that have tremendous potential for the production of a broad spectrum of fully human antibodies,” remarks Jeffrey Riley, Synthetic Biologics’ CEO. “This expanded relationship gives us access to this paradigm-changing platform.”

The latest Synthetic Biologics agreement is the second for Intrexon this month. Last week the firm inked an exclusive research collaboration with BioLife Cell Bank, focused on leveraging Intrexon’s technologies to develop autologous, genetically modified stem cell therapeutics for spinal muscular atrophy. And a few weeks earlier the firm inked an alliance with Oragenics through which the latter intends to develop broad spectrum lantibiotic candidates against infectious diseases in humans and companion animals."
http://bit.ly/Nk13Um


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Career Girls: Mathematician "Bioinformatics"

This clip is part the Career Girls ongoing series of career guidance/inspiration videos.
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Synthetic Biology Applications Inventory

Synthetic Biology Applications Inventory | Bioinformatics Training | Scoop.it
This new inventory begins to track the impact of synthetic biology on a wide range of applications, from energy and pharmaceuticals to chemicals and food ingredients.

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Openly Streamlining Peer Review | PLOS Biologue

Openly Streamlining Peer Review | PLOS Biologue | Bioinformatics Training | Scoop.it

http://bit.ly/Ma0E9e


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20 years and counting

20 years and counting | Bioinformatics Training | Scoop.it
GCC bioinformatics training grant wins fifth competitive renewal. One of the Texas Medical Center's (TMC) longest-running federal grants — a training grant for pre- and postdoctoral fellows in biomedical informatics that was ...
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CAP publishes revised version of molecular pathology checklist with dedicated ... - News-Medical.net

CAP publishes revised version of molecular pathology checklist with dedicated ...News-Medical.netThe College of American Pathologists (CAP) published a revised version of its molecular pathology checklist with a dedicated section on next generation...
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Many medical schools don't have guidelines for training students about electronic health records

The electronic health record (EHR) has improved health care delivery, but also has presented a challenge for medical student training. Educational mandates that can provide guidelines to medical schools on how to teach and assess student skills in EHR proficiency do not exist.

 

In two studies published this month by the journal Teaching and Learning in Medicine, the Alliance for Clinical Education describes the importance of medical student participation in the EHR. The Alliance, made up of education leaders from a broad range of medical specialties, was formed to enhance clinical instruction of medical students.

 

“Currently only 64 percent of medical school programs allow students any use of EHRs, and of those only two-thirds allowed students to write notes with in the electronic record,” says Maya M. Hammoud, the study’s lead author and associate professor of Obstetrics and Gynecology at the University of Michigan Medical School.

 

“Previously, students were just able to pick up a physical patient chart. Now they need permission to use hospital computers and passwords to access the EHR. There also are concerns surrounding Medicare rules about physicians using trainees’ findings in the HER,” says Hammoud, who is chair of the Alliance’s Research Committee.


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James J. Collins, Ph.D. » Biomedical Engineering | Boston University

James J. Collins, Ph.D. » Biomedical Engineering | Boston University | Bioinformatics Training | Scoop.it

Congratulations to Jim Collins, BU Innovator of the Year & father of synthetic biology

http://www.bu.edu/bme/people/primary/collins/


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