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
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:/
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
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 , 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 »
Hull, D., Pettifer, S., & Kell, D. (2008) Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web. PLoS Computational Biology, 4(10). DOI: 10.1371/journal.pcbi.1000204
Attwood, T., Kell, D., McDermott, P., Marsh, J., Pettifer, S., & Thorne, D. (2010) Utopia documents: linking scholarly literature with research data. Bioinformatics, 26(18). DOI: 10.1093/bioinformatics/btq383
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 »
Capone, B., Coluzza, I., LoVerso, F., Likos, C., & Blaak, R. (2012) Telechelic Star Polymers as Self-Assembling Units from the Molecular to the Macroscopic Scale. Physical Review Letters, 109(23). DOI: 10.1103/PhysRevLett.109.238301
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:/
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 »
Fahn, C., & Sun, H. (2010) Development of a Fingertip Glove Equipped with Magnetic Tracking Sensors. Sensors, 10(2), 1119-1140. DOI: 10.3390/s100201119
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
HOSHINO, K. (2006) Dexterous Robot Hand Control with Data Glove by Human Imitation. IEICE Transactions on Information and Systems, E89-D(6), 1820-1825. DOI: 10.1093/ietisy/e89-d.6.1820
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
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 »
Bay, A., André, N., Sarrazin, M., Belarouci, A., Aimez, V., Francis, L., & Vigneron, J. (2013) Optimal overlayer inspired by Photuris firefly improves light-extraction efficiency of existing light-emitting diodes. Optics Express, 21(S1). DOI: 10.1364/OE.21.00A179
Bay, A., Cloetens, P., Suhonen, H., & Vigneron, J. (2013) Improved light extraction in the bioluminescent lantern of a Photuris firefly (Lampyridae). Optics Express, 21(1), 764. DOI: 10.1364/OE.21.000764
What is the difference between primary, secondary and higher education?... Read more »
Martin, F. (2012) Will massive open online courses change how we teach?. Communications of the ACM, 55(8), 26. DOI: 10.1145/2240236.2240246
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 »
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 »
Han, S., Bae, H., Kim, J., Shin, S., Choi, S., Lee, S., Kwon, S., & Park, W. (2012) Lithographically Encoded Polymer Microtaggant Using High-Capacity and Error-Correctable QR Code for Anti-Counterfeiting of Drugs. Advanced Materials, 24(44), 5924-5929. DOI: 10.1002/adma.201201486
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 »
Collins, B., Li, Z., Tumbleston, J., Gann, E., McNeill, C., & Ade, H. (2012) Absolute Measurement of Domain Composition and Nanoscale Size Distribution Explains Performance in PTB7:PC BM Solar Cells . Advanced Energy Materials. DOI: 10.1002/aenm.201200377
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 »
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
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
Volkov AG, Adesina T, & Jovanov E. (2007) Closing of venus flytrap by electrical stimulation of motor cells. Plant signaling , 2(3), 139-45. PMID: 19516982
Kindt M, Soeter M, & Vervliet B. (2009) Beyond extinction: erasing human fear responses and preventing the return of fear. Nature neuroscience, 12(3), 256-8. PMID: 19219038
Kim IJ, Zhang Y, Yamagata M, Meister M, & Sanes JR. (2008) Molecular identification of a retinal cell type that responds to upward motion. Nature, 452(7186), 478-82. PMID: 18368118
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
Kraskov A, Dancause N, Quallo MM, Shepherd S, & Lemon RN. (2009) Corticospinal neurons in macaque ventral premotor cortex with mirror properties: a potential mechanism for action suppression?. Neuron, 64(6), 922-30. PMID: 20064397
Blackiston DJ, Silva Casey E, & Weiss MR. (2008) Retention of memory through metamorphosis: can a moth remember what it learned as a caterpillar?. PloS one, 3(3). PMID: 18320055
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
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
Fu M, Yu X, Lu J, & Zuo Y. (2012) Repetitive motor learning induces coordinated formation of clustered dendritic spines in vivo. Nature, 483(7387), 92-5. PMID: 22343892
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:/
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 »
Atri, D., DeMarines, J., & Haqq-Misra, J. (2011) A protocol for messaging to extraterrestrial intelligence. Space Policy, 27(3), 165-169. DOI: 10.1016/j.spacepol.2011.01.001
Edmondson, W. (2010) Targets and SETI: Shared motivations, life signatures and asymmetric SETI. Acta Astronautica, 67(11-12), 1410-1418. DOI: 10.1016/j.actaastro.2010.01.017
As you get ready to celebrate the New Year, you’ve likely come across articles about different food ‘cures’ that can prevent or reduce alcohol hangovers. Aside from anecdotic ‘evidence’ that [...]... Read more »
B.-Y. KIM, Z.-G. CUI, S.-R. LEE, S.-J. KIM, H.-K. KANG, Y.-K. LEE, & D.-B. PARK. (2009) Effects of Asparagus ofﬁcinalis Extracts on Liver Cell Toxicity and Ethanol Metabolism. JOURNAL OF FOOD SCIENCE. info:/10.1111/j.1750-3841.2009.01263.x
Wind power is free, which is why German engineers have been experimenting with a device they termed SkySails. They’ve proved that inflatable kites can actually haul freighters across the ocean. This mirrors research conducted over 20 years ago by a Japanese firm. Those who say that sails aren’t a new emerging technology should be careful, [...]... Read more »
M. Canale, L. Fagiano, M. Milanese, & V. Razza. (2010) Control of tethered airfoils for sustainable marine transportation IEEE Conference on Control Applications - CCA. IEEE Conference on Control Applications - CCA , 1904-1909. DOI: 10.1109/CCA.2010.5611085
And now, the next step in neuron building! You can see all the previous steps and shortcuts here. Step 4 is adding intrinsic channels to your neuron.Potassium Channel (source)Pretty much all neurons need sodium and potassium channels so they can fire action potentials, but other channels such as calcium channels are also commonly seen in computational models. To add these channels you have to extract the parameters from known data. This means extracting Boltzmann curves and time constant information so you can tell the channel which voltages activate it and inactivate it and how fast to open and close. Activation (Boltzmann) curve for fast sodium channelThis step is tricky and can take a long time, but there is some software that can help. The Enguage Digitizer is one tool I could not live without. Enguage is basically a tool that allows you to manually trace curves from published figures to get the curve data as an excel or .csv file. First you add axis points using the button at the top that has red plus signs on it. You tell the software what values each of the 3 corners of the graph are. Then you click the blue plus signs button and start to trace your graph, like so:using Enguage digitizer to extract channel dataThen you export the data as whichever type of file you want. Pretty nice!I like to have the data this way because then I can overlay this figure trace with any other trace I want and can manually fit an equation to it.Channels are a hugely important part of a computational model. A recent paper from Eve Marder's lab shows that even with a very simple morphological model (just a soma), interesting electrical characteristics can be seen simply by manipulating the channels. Kispersky et al., 2012 from Figure 1Kispersky et al., (2012) introduce an interesting paradox. They show that when you increase the sodium channel conductance you see more action potentials with low current injections (like 200pA). This is expected because the sodium channel is what causes the upswing of the action potential and more sodium is thought to mean more excitability. However, the authors find that when a high current injection is given (like 10nA), the increased sodium channel conductance actually decreases the firing rate. This is counter-intuitive because it goes against the more sodium=more excitability rule.This is a pretty cool finding published in the Journal of Neuroscience using only a simple one-compartment model. The finding is based entirely on channel manipulation, and demonstrates how important these intrinsic channels are to any computational model. © TheCellularScaleKispersky TJ, Caplan JS, & Marder E (2012). Increase in sodium conductance decreases firing rate and gain in model neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience, 32 (32), 10995-1004 PMID: 22875933... Read more »
Kispersky TJ, Caplan JS, & Marder E. (2012) Increase in sodium conductance decreases firing rate and gain in model neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience, 32(32), 10995-1004. PMID: 22875933
A neurobiology team at the University of Pittsburgh has given a Jan Scheuermann the power to do something that a degenerative disease had taken away. Thanks to a brain-computer interface and a robotic arm she affectionately calls “Hector,” Jan is now able to feed herself, despite her paralysis.... Read more »
Collinger, J., Wodlinger, B., Downey, J., Wang, W., Tyler-Kabara, E., Weber, D., McMorland, A., Velliste, M., Boninger, M., & Schwartz, A. (2012) High-performance neuroprosthetic control by an individual with tetraplegia. The Lancet. DOI: 10.1016/S0140-6736(12)61816-9
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