Post List

Computer Science / Engineering posts

(Modify Search »)

  • January 29, 2013
  • 07:31 PM
  • 343 views

Microstructure of Film Coated Tablets

by Axel Zeitler in Pharmaceutical Solid State Research Cluster (PSSRC)

Since 2007 when terahertz pulsed imaging (TPI) was first developed to non-destructively measure the coating thickness of pharmaceutical tablets there has been intense research in the PSSRC into how this technique can help improve the quality of pharmaceutical coatings and thus make controlled release technology based on coatings of single dosage forms attractive to industry.... Read more »

Brock, D., Zeitler, J., Funke, A., Knop, K., & Kleinebudde, P. (2012) A comparison of quality control methods for active coating processes. International Journal of Pharmaceutics, 439(1-2), 289-295. DOI: 10.1016/j.ijpharm.2012.09.021  

  • January 24, 2013
  • 04:45 AM
  • 457 views

Storage and successful retrieval of a huge amount of data utilizing DNA strands

by Usman Paracha in SayPeople

Researchers have converted the dream of a huge amount of DNA storage and its accurate retrieval into reality.

This research has been published online in the journal Nature.

In this research, scientists have successfully stored an audio file of 26 seconds from the Martin Luther King's 1963 "I have a dream" speech on the adenine, thymine, cytosine and guanine components of synthesized DNA. Not only had this but they also stored all 154 of Shakespeare's sonnets, a digital photo of their laboratory and the famous paper of James Watson and Francis Crick about the description of double-stranded DNA on DNA. This research presented the storage of huge amount of 2.2 petabytes of data per gram of DNA.

"We already know that DNA is a robust way to store information because we can extract it from wooly mammoth bones, which date back tens of thousands of years, and make sense of it,” Dr Nick Goldman of EMBL-European Bioinformatics Institute (EMBL-EBI), said in a statement. “It’s also incredibly small, dense and does not need any power for storage, so shipping and keeping it is easy.”

Previously scientists from Harvard University reported the storage of 704 terabytes of data in a gram of DNA and the research was published in the journal Science.

Scientists, in this study, also corrected the errors on previous DNA-encoding techniques and accurately regained 100% information. In order to do this, scientists reserved one of the letters to break up the long runs of any of the other three bases.

Generalized approach to the storage of the data on DNA (Credit: Goldman et al., Nature)
DNA storage is highly anticipated because memory in DNA could be stored for thousands of years without special storage requirements such as cold, dark and/or dry. It is proposed that one gram of single-stranded DNA can store nearly 100 billion DVDs of data that can help to store a huge amount of data by large organizations such as CERN in a small place.

“We’ve created a code that's error tolerant using a molecular form we know will last in the right conditions for 10 000 years, or possibly longer,” Nick said. “As long as someone knows what the code is, you will be able to read it back if you have a machine that can read DNA.”

Although, this storage technique is highly efficient but is also very much costly.

Reference:

Goldman, N., Bertone, P., Chen, S., Dessimoz, C., LeProust, E., Sipos, B., & Birney, E. (2013). Towards practical, high-capacity, low-maintenance information storage in synthesized DNA Nature DOI: 10.1038/nature11875... Read more »

  • January 23, 2013
  • 07:38 AM
  • 903 views

Sending Odors and Tastes as an Email Attachment

by Jason Carr in Wired Cosmos

Research into cybernetic organs has been largely focused on replacements for disabled individuals who have lost a limb. Electronic noses and tongues are designed for a radically different purpose. Humans perceive different chemicals as various tastes and odors. Many types of additives are industrially manufactured to replicate certain flavors or scents. Electronic noses and tongues [...]... Read more »

  • January 22, 2013
  • 03:54 PM
  • 560 views

These dudes figured out how to identify supposedly anonymous people whose genomes are publically available

by Sick Papes in Sick Papes

Super nasty genome hacking I CANT BELIEVE IT!!... Read more »

Gymrek M, McGuire AL, Golan D, Halperin E, & Erlich Y. (2013) Identifying personal genomes by surname inference. Science (New York, N.Y.), 339(6117), 321-4. PMID: 23329047  

  • January 22, 2013
  • 04:09 AM
  • 707 views

ToxBank: the next generation toxicology

by egonw in Chem-bla-ics

Before I moved to my current position in Maastricht, I had the great pleasure to work with Prof. Roland Grafström (check his pathway bioinformatics done with his then PhD Rebecca) and Prof. Bengt Fadeel at the Karolinska Institutet. During this year I part-time worked on ToxBank and part-time on nano-QSAR, and worked on semantics, predictive toxicology, and Open Data. This blog post is about the ToxBank work.



I promised firework, and the first rockets are heading upwards: a key ToxBank paper has now been published in Molecular Informatics. Pekka Kohonen wrote up a nice overview of the ToxBank project, the current platform (based on RDF, REST, ISATab, and OpenTox (my archives)), and the test compounds that the SEURAT-1 cluster identified. Various bioinformatics approaches were used to visualize the diversity of the selected compounds. The idea is that the all EU FP7 projects in the SEURAT-1 cluster (consisting of six consortia) will test at least these compounds, creating a rich data set of toxicology-related data for these compounds.

As a temporary, quick solution I proposed the Semantic MediaWiki to create a semantic knowledge base, which was extensively and very productively continued by David from Leadscope. This way, we could easily list all compounds, by doing a search, rather than manually adding them:




Each compound has extensive information on the mode of action, physicochemical properties and more (such as here for acetaminophen):




All this information is available as semantic data. For example, check this link. Network and Gene Ontology analyses on these compounds have been performed, and presented in the paper, further confirming the diversity of the compound set. This leads to possible integration of their work with WikPathways and PathVisio, and I will do my best to get the right people talking to each other.

The ToxBank project further develops Open Source software for an online data warehouse for hosting experimental data on these compounds. A mix of approaches is used here to base their warehouse on, including OpenTox (RDF and REST(-like)-based), ISATab, and various ontologies.

In designing their software, they use a pretty unique approach for EU projects, based on formal requirement analyses protocols, resulting in a user-oriented platform. Now, there is much to say about who the user is, and in fact, there are multiple user types, called personas, and ToxBank takes that idea into account.

Therefore, in many ways, ToxBank is, in my humble but somewhat biased opinion, a project that leads the (predictive) toxicology community into a new era. Congratulations to the full ToxBank consortium! It was great being part of it!

Kohonen, P., Benfenati, E., Bower, D., Ceder, R., Crump, M., Cross, K., Grafström, R., Healy, L., Helma, C., Jeliazkova, N., Jeliazkov, V., Maggioni, S., Miller, S., Myatt, G., Rautenberg, M., Stacey, G., Willighagen, E., Wiseman, J., & Hardy, B. (2013). The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing Molecular Informatics DOI: 10.1002/minf.201200114... Read more »

Kohonen, P., Benfenati, E., Bower, D., Ceder, R., Crump, M., Cross, K., Grafström, R., Healy, L., Helma, C., Jeliazkova, N.... (2013) The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing. Molecular Informatics. DOI: 10.1002/minf.201200114  

  • January 20, 2013
  • 12:00 PM
  • 657 views

New nanotech fiber: Robust handling, shocking performance

by Perikis Livas in Chilon

Rice University’s latest nanotechnology breakthrough was more than 10 years in the making, but it still came with a shock. Scientists from Rice, the Dutch firm Teijin Aramid, the U.S. Air Force and Israel’s Technion Institute this week unveiled a new carbon nanotube (CNT) fiber that looks and acts like textile thread and conducts electricity and heat like a metal wire. In this week’s issue of Science, the researchers describe an industrially scalable process for making the threadlike fibers, which outperform commercially available high-performance materials in a number of ways.... Read more »

Jade Boyd. (2013) New nanotech fiber: Robust handling, shocking performance. Rice University News. info:/

  • January 18, 2013
  • 09:47 AM
  • 553 views

On "Join Papester Collective 1.0: How to reply to #icanhazpdf in 3 seconds"

by Eugenio Maria Battaglia in Science to Grok

I'm totally supporting this potential system theorized some days ago by Micah Allen and his friend Hauke on Allen's Neuroconscience blog . They discuss a quick and reliable strategy to share papers behind a paywall.
The proposed system is really easy and accessible by everyone, since it uses particular twitter's #hashtags for query and response.
I strongly believe that what started after Aaron Swartz's dead with #pdftribute, and continued with #sharecredentials (unfortunately and strangely still not so shared on twitter), and now followed by #icanhazpdf / #papester will quickly lead to a massive weaken of paywall systems. Therefore, this will push people to understand and to propose alternative ways that are more ethically correct and also apt to current science needs.... Read more »

Cook, J., & Attari, S. (2012) Paying for What Was Free: Lessons from the Paywall . Cyberpsychology, Behavior, and Social Networking, 15(12), 682-687. DOI: 10.1089/cyber.2012.0251  

  • January 17, 2013
  • 01:54 PM
  • 749 views

How to export, delete and replace your Mendeley account and library

by Duncan Hull in O'Really?

News that Reed Elsevier is in talks to buy Mendeley.com will have many scientists reaching for their “delete account” button. Mendeley has built an impressive user-base of scientists and other academics since they started, but the possibility of an Elsevier takeover has worried some of its users. Elsevier has a strained relationship with some groups in the scientific community [1], so it will be interesting to see how this plays out.

If you’ve built a personal library of scientific papers in Mendeley, you won’t just want to delete all the data, you’ll need to export your library first, delete your account and then import it into a different tool.

Disclaimer: I’m not advocating that you delete your account, just that if you do decide to, here’s how to do it, and some alternatives to consider.... Read more »

  • January 17, 2013
  • 10:15 AM
  • 820 views

Soft Lego Built in the Computer

by Jason Carr in Wired Cosmos

Barbara Capone of the Computational Physics Group of the University of Vienna has developed a new method for the construction of building blocks at the nanoscale. The researcher in Soft Matter Physics, who works at the group of Christos Likos, Professor for Multiscale Computational Physics, is specialized on topics of self-assembly of materials at the [...]... Read more »

  • January 16, 2013
  • 04:11 PM
  • 594 views

Oscar-worthy smoke signals

by Perikis Livas in Chilon

Top honour for ETH-Zurich professor and Disney director Markus Gross: he is to receive a “Tech Oscar” from the Academy of Motion and Picture Arts and Sciences (AMPAS) along with three other computer scientists for a procedure they developed which leading special effects studios now use to simulate smoke and explosions in Hollywood films.... Read more »

Peter Rüegg. (2013) Oscar-worthy smoke signals. ETH Life. info:/

  • January 16, 2013
  • 02:24 AM
  • 903 views

Show Some Love for the Data Glove

by Jason Carr in Wired Cosmos

Data Gloves (or wired gloves or cybergloves), as the name implies, are computer input devices that are worn on the hand like a glove. They utilize motion trackers to translate finger manipulations into electrical signals. In the near future, this technology might revolutionize the way that disabled people are able to access computer resources. For [...]... Read more »

Yamaura H, Matsushita K, Kato R, & Yokoi H. (2009) Development of hand rehabilitation system for paralysis patient - universal design using wire-driven mechanism. Conference proceedings : .. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference, 7122-5. PMID: 19963950  

Dalley, S., Varol, H., & Goldfarb, M. (2012) A Method for the Control of Multigrasp Myoelectric Prosthetic Hands. IEEE Transactions on Neural Systems and Rehabilitation Engineering, 20(1), 58-67. DOI: 10.1109/TNSRE.2011.2175488  

  • January 14, 2013
  • 10:52 PM
  • 374 views

Brighter LEDs bioinspired from fireflies

by Cath in Basal Science (BS) Clarified

A team of researchers from Belgium, Canada, and France have developed a more efficient gallium nitride (GaN)-based LED using a design inspired by the firefly. The design, fabrication, and characterization of this [...]... Read more »

  • January 11, 2013
  • 11:59 AM
  • 775 views

A joke about teaching and learning via Jason Bangbala

by Duncan Hull in O'Really?

What is the difference between primary, secondary and higher education?... Read more »

Vardi, M. (2012) Will MOOCs destroy academia?. Communications of the ACM, 55(11), 5-5. DOI: 10.1145/2366316.2366317  

Khan, S. (2013) What college could be like. Communications of the ACM, 56(1), 41. DOI: 10.1145/2398356.2398370  

  • January 9, 2013
  • 04:00 PM
  • 378 views

Controlling variability - Likelihood calculus paper series review part 1

by Travis DeWolf in studywolf

Dr. Terry Sanger has a series of papers that have come out in the last few years describing what he has named ‘likelihood calculus’. The goal of these papers is to develop a ‘a theory of optimal control for variable, uncertain, and noisy systems that nevertheless accomplish real-world tasks reliably.’ The idea being that successful performance can be thought of as modulating variance of movement, allocating resources to tightly control motions when required and allowing variability in task-irrelevant dimensions. To perform variability modulation, we first need a means of capturing mathematically how the features of an uncertain controller operating affect variability in system movement. Defining terms quickly, the features of a controller are the different components that produce signals resulting in movement, variability is taken here to be the trial-to-trial variation in movements, and uncertainty means that the available sensory feedback does not uniquely determine the true state of the world, where uncertainty can arise from noise on sensory feedback signals, unmodeled dynamics, and/or quantitization of sensory feedback. To capture all this uncertainty and variability, probability theory will naturally be employed. In this post I will review the paper ‘Controlling variability’ (2010) by Dr. Sanger, which sets up the framework for describing the time course of uncertainty during movement.... Read more »

Sanger TD. (2010) Controlling variability. Journal of motor behavior, 42(6), 401-7. PMID: 21184358  

  • January 7, 2013
  • 09:24 PM
  • 462 views

QR Codes to be used to prevent drug counterfeiting

by Cath in Basal Science (BS) Clarified

Think Quick Response (QR) codes are just for advertising products or transferring addresses and contact information between smartphones? Well, it turns out they can also be used to prevent drug [...]... Read more »

  • January 7, 2013
  • 02:27 PM
  • 731 views

New Path to More Efficient Organic Solar Cells

by Jason Carr in Wired Cosmos

Why are efficient and affordable solar cells so highly coveted? Volume. The amount of solar energy lighting up Earth’s land mass every year is nearly 3,000 times the total amount of annual human energy use. But to compete with energy from fossil fuels, photovoltaic devices must convert sunlight to electricity with a certain measure of [...]... Read more »

  • January 4, 2013
  • 11:43 AM
  • 828 views

The Science of Choosing Space Pioneers

by Jason Carr in Wired Cosmos

I often ask others if they would live in space or on another planet if given the opportunity. More often than not, the answer is in the affirmative. But what if you were given the chance and actually wanted to go, but were declined because you weren’t selected by a computer algorithm as one of [...]... Read more »

Yusof, N., & van Loon, J. (2012) Engineering a Global City: The Case of Cyberjaya. Space and Culture, 15(4), 298-316. DOI: 10.1177/1206331212453676  

Saaty, T., & Sagir, M. (2012) Global awareness, future city design and decision making. Journal of Systems Science and Systems Engineering, 21(3), 337-355. DOI: 10.1007/s11518-012-5196-z  

  • January 4, 2013
  • 10:44 AM
  • 1,243 views

Cellular Recap of 2012 #2: favorites

by TheCellularScale in The Cellular Scale

As promised, here are my favorite posts from each month.January: The Human Neuron" not so special after all?Butti C, Santos M, Uppal N, & Hof PR (2011). Von Economo neurons: Clinical and evolutionary perspectives. Cortex; a journal devoted to the study of the nervous system and behavior PMID: 22130090February: If you give a mouse a placebo...Wise RA, Wang B, & You ZB (2008). Cocaine serves as a peripheral interoceptive conditioned stimulus for central glutamate and dopamine release. PloS one, 3 (8) PMID: 18682722 March: Plant neurons: Sensation and Action in the Venus FlytrapBenolken RM, & Jacobson SL (1970). Response properties of a sensory hair excised from Venus's flytrap. The Journal of general physiology, 56 (1), 64-82 PMID: 5514161Volkov AG, Adesina T, & Jovanov E (2007). Closing of venus flytrap by electrical stimulation of motor cells. Plant signaling & behavior, 2 (3), 139-45 PMID: 19516982 Forterre Y, Skotheim JM, Dumais J, & Mahadevan L (2005). How the Venus flytrap snaps. Nature, 433 (7024), 421-5 PMID: 15674293... Read more »

Butti C, Santos M, Uppal N, & Hof PR. (2011) Von Economo neurons: Clinical and evolutionary perspectives. Cortex; a journal devoted to the study of the nervous system and behavior. PMID: 22130090  

Benolken RM, & Jacobson SL. (1970) Response properties of a sensory hair excised from Venus's flytrap. The Journal of general physiology, 56(1), 64-82. PMID: 5514161  

Forterre Y, Skotheim JM, Dumais J, & Mahadevan L. (2005) How the Venus flytrap snaps. Nature, 433(7024), 421-5. PMID: 15674293  

Kay JN, De la Huerta I, Kim IJ, Zhang Y, Yamagata M, Chu MW, Meister M, & Sanes JR. (2011) Retinal ganglion cells with distinct directional preferences differ in molecular identity, structure, and central projections. The Journal of neuroscience : the official journal of the Society for Neuroscience, 31(21), 7753-62. PMID: 21613488  

Casile A, Caggiano V, & Ferrari PF. (2011) The mirror neuron system: a fresh view. The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry, 17(5), 524-38. PMID: 21467305  

Marx M, Günter RH, Hucko W, Radnikow G, & Feldmeyer D. (2012) Improved biocytin labeling and neuronal 3D reconstruction. Nature protocols, 7(2), 394-407. PMID: 22301777  

Finger TE, & Kinnamon SC. (2011) Taste isn't just for taste buds anymore. F1000 biology reports, 20. PMID: 21941599  

Triana-Del Rio R, Montero-Domínguez F, Cibrian-Llanderal T, Tecamachaltzi-Silvaran MB, Garcia LI, Manzo J, Hernandez ME, & Coria-Avila GA. (2011) Same-sex cohabitation under the effects of quinpirole induces a conditioned socio-sexual partner preference in males, but not in female rats. Pharmacology, biochemistry, and behavior, 99(4), 604-13. PMID: 21704064  

Labour MN, Banc A, Tourrette A, Cunin F, Verdier JM, Devoisselle JM, Marcilhac A, & Belamie E. (2012) Thick collagen-based 3D matrices including growth factors to induce neurite outgrowth. Acta biomaterialia, 8(9), 3302-12. PMID: 22617741  

  • January 4, 2013
  • 02:14 AM
  • 629 views

Sweet Science

by Emarkham in GeneticCuckoo

A look at the new fun approach and interest taken in science and how this is being marketed and aimed at young people. ... Read more »

E Markham. (2013) Sweet Science. Blogspot. info:/

  • January 1, 2013
  • 02:27 PM
  • 736 views

Reaching E.T. Through Standardized Protocols

by Jason Carr in Wired Cosmos

Choosing a single telecommunications protocol has always been difficult for engineers on Earth, so it’s especially difficult for those who want to communicate with beings from another star system. While it’s nice to imagine that extraterrestrial beings would be able to interface with whatever protocol humans decide to encode a message in, that’s not a [...]... Read more »

join us!

Do you write about peer-reviewed research in your blog? Use ResearchBlogging.org to make it easy for your readers — and others from around the world — to find your serious posts about academic research.

If you don't have a blog, you can still use our site to learn about fascinating developments in cutting-edge research from around the world.

Register Now

Research Blogging is powered by SMG Technology.

To learn more, visit seedmediagroup.com.