Computer Science / Engineering posts
- April 17, 2010
- 12:31 AM
- 1,557 views
Using the fact that sometimes scientists look at the pictures first
by Christina Pikas in Christina's LIS Rant
I was happy to see that the authors published this article in PlosOne. I was following their work a while ago, but had lost track (plus, when asked, the last author implied that they had moved on to new projects). So here's the citation and then I'll summarize and comment. Divoli, A., Wooldridge, M., & Hearst, M. (2010). Full Text and Figure Display Improves Bioscience Literature Search PLoS ONE, 5 (4) DOI: 10.1371/journal.pone.0009619 The authors created a prototype information system that used Lucene to index the metadata for open access biomed articles, the full text, and the captions for images and tables. The interface is set up to allow you to use one search box and then radio buttons to select full text and abstracts, figure captions, or tables. In the first, the results are sort of like the standard metadata and abstract with key word in context excerpts and extracted images. For figure captions, you can either have a grid of figures, or a list. For tables, you get a citation, the table caption, and the table. The article spends a good deal of time discussing design decisions, providing a tutorial for creating your own. To build the prototype, they got the XML from PubMed Central, pulled out authors, images, captions, abstracts... They made different sizes of the images for quick retrieval later.They then included different fields with different weights depending on what you select to search. They then got a group of biologists (n=20 although number isn't really important for qualitative studies), and ran them through a study. The participants provided the query and looked at it in each view, thinking aloud about their reactions and steps. They were then asked a few questions about each interface The majority of the participants would choose to use this type of interface for at least some of their searching. Seems like they got the full text search, but were not quite as sure about the table search. Some thought it would be useful for getting right to the results but several didn't think they would use it. Now for some commentary... I was somewhat critical in my post I linked to above, but I really think this is promising stuff. The authors point out that this is very dependent on access to the full text and also won't be universally useful. There are plenty of search situations in which the images wouldn't be used, but they should be an option. Since my earlier post, CSA has added "deep indexing" to more of their files. It's not the same as their dedicated Illustrata product, which is more like Biotext. Publishers have the full text, so some of them are also making the images and tables available outside of the article. For example, both ACS and RSC have added images to their RSS feeds. ScienceDirect has a tables and images tab on their articles - which is nice for scanning to see if the article is relevant. PlosOne lets you look through a list of the tables and images, download a ppt or high quality image. Springer Images also lets you search the tables and captions to get pictures. It also indexes the context of the reference to the image in the text. You also get a link to the article and excerpts like on Google Books. My colleague at work pointed out that it is useful for finding phase diagrams. But more than all of that, there's been a lot of talk recently about disaggregating the journal article or even doing away with the whole and just using the pieces. If so, maybe this is an intermediate step. Read the comments on this post...... Read more »
Divoli, A., Wooldridge, M., & Hearst, M. (2010) Full Text and Figure Display Improves Bioscience Literature Search. PLoS ONE, 5(4). DOI: 10.1371/journal.pone.0009619
- April 15, 2010
- 02:21 AM
- 1,808 views
Online Trust and it’s Antecedents
by Dr Shock in Dr Shock MD PhD
We’ve discussed the use of online shopping and gender previously. Especially women are skeptical towards online shopping, they tend to fear risks and threats associated with online shopping. The acceptance of online transactions depend on the perceived risks involved, the technology used for the online transactions and the organizations as the other parties in the [...]
Related posts:Women Online Shopping: Shop Until You Drop?
Finding Credible Health Information Online: MedLibs Round 1.8
Assess Health Information Online
... Read more »
Beldad, A., de Jong, M., & Steehouder, M. (2010) How shall I trust the faceless and the intangible? A literature review on the antecedents of online trust. Computers in Human Behavior. DOI: 10.1016/j.chb.2010.03.013
- April 15, 2010
- 01:05 AM
- 651 views
An interview with the creator of BioTorrents
by Morgan Langille in Beta Science
Who better to interview the creator of BioTorrents than the creator himself? :)Interviewer: So Morgan, your article entitled “BioTorrents: A File Sharing Service for Scientific Data” was published today in PLoS One. BioTorrents uses the popular peer-to-peer file sharing protocol, BitTorrent, to allow scientists to rapidly share their results, datasets, and software. Where did this idea come from?Morgan: Well about 6 months ago I was downloading some genome files from NCBI's FTP site and was watching the download speed hover between 50-100Kb/s and I said to myself (much like this interview) I wish could download these with BitTorrent. I have used BitTorrent for downloading other non-scientific data (lets not discuss what they may be) and I know it is a much faster and more reliable way for getting large files. A few minutes later I posted to Twitter asking if anyone had thought about setting up a BitTorrent tracker for scientific data and the response was over-whelming (well only 1 response, but I could feel it had a larger impact). About a week later, I brought up the idea again over coffee with some members of my lab and more importantly my post-doc supervisor Dr. Jonathan Eisen. He thought it was a good idea and well worth pursuing, which was all I needed to push aside all my other "real" research and focus on this much more "fun" project.Interviewer: Thanks for that long-winded response. Maybe you could comment more briefly on the benefits of using BioTorrents/BitTorrent for sharing scientific data.Morgan: I think it is explained fairly well in the manuscript and in my previous blog post, but to reiterate the major benefits are:1) Faster, more reliable, and better controlled downloading of data that scales well for very large files.2) Instant "publishing" of data, results, and software.3) Very easy for anyone to share their data. No dedicated web server needed.Interviewer: Who should consider sharing data on BioTorrents?Morgan: Everyone that has something to share. Large institutions can benefit from reduced bandwidth requirements, while individual users can benefit from the simplicity of sharing with BitTorrent technology. Personally, I really like the idea of open data and the idea of sharing results before publication. How many times has someone done an all vs all blast of microbial genomes? In theory this can be done once, and that person can be recognized (referenced, co-authored, etc.) when other researchers use that data.Interviewer: Are there any challenges/limitations to using BitTorrent with scientific data?Morgan: BitTorrent excels at transferring very large popular datasets. Therefore, if only one person is "seeding" a file and only one person is downloading the file most of the advantage to using BitTorrent is lost. However, even in this worst case scenario, the transfer speed would be roughly equivalent to using traditional file transfer methods such as FTP/HTTP and BitTorrent still provides the benefit of error checking and ease of data transfer control (pause, resume, etc.). Another possible problem is that some institutions often try to limit BitTorrent traffic since it is often considered illegal non-work related network traffic. However, I would encourage users at these institutions to explain to their network administrator that many times BitTorrent traffic is legitimate and shouldn't be blocked.Interviewer: Why publish in PLoS One?Morgan: I have been a big fan of the PLoS One journal and ever since I blogged about it last year "Is PLOS One the future of scientific publishing?", I have been wanting to submit a paper there. Also, considering that BioTorrents is aimed at improving open access to data in all fields of science, PLoS One seemed like the most obvious journal choice for our manuscript.Langille, M., & Eisen, J. (2010). BioTorrents: A File Sharing Service for Scientific Data PLoS ONE, 5 (4) DOI: 10.1371/journal.pone.0010071... Read more »
Langille, M., & Eisen, J. (2010) BioTorrents: A File Sharing Service for Scientific Data. PLoS ONE, 5(4). DOI: 10.1371/journal.pone.0010071
- April 13, 2010
- 10:37 AM
- 772 views
Five Users Do Not Make a Study
by Simon Harper in Thinking Out Loud
It is widely assumed that 5 participants suffice for usability testing. In this study, 60 users were tested and random sets of 5 or more were sampled from the whole, to demonstrate the risks of using only 5 participants and the benefits of using more. Some of the randomly selected sets of 5 participants found 99% of the problems; other sets found only 55%. With 10 users, the lowest percentage of problems re-vealed by any one set was increased to 80%, and with 20 users, to 95%. [Faulkner, 2003]... Read more »
Nielsen, J. (1993) Usability engineering. Book. info:/
Faulkner L. (2003) Beyond the five-user assumption: benefits of increased sample sizes in usability testing. Behavior research methods, instruments, , 35(3), 379-83. PMID: 14587545
- April 7, 2010
- 10:56 AM
- 1,435 views
I never metagenomics I didn’t like
by Iddo Friedberg in Byte Size Biology
“Let another man praise thee, and not thine own mouth; a stranger, and not thine own lips.” — Proverbs 27:2
“What-ever” – Me
In PLoS Computational Biology this week, a trio of researchers provides a review of the challenges that metagenomics might ― and already do ― pose for bioinformaticians. The authors refer to metagenomic sequencing data [...]... Read more »
Wooley, J., Godzik, A., & Friedberg, I. (2010) A Primer on Metagenomics. PLoS Computational Biology, 6(2). DOI: 10.1371/journal.pcbi.1000667
- April 6, 2010
- 09:00 AM
- 763 views
Antivirus without the software
by David Bradley in Sciencetext
UK research suggests that approximately 97% of businesses have an internet connection and the vast majority of those are now using broadband access. The same research also found that infection with computer viruses, spyware, worms, Trojans, and other malicious software was the biggest single cause of security incidents, accounting for about half of all incidents, [...]Post from: David Bradley's Sciencetext Tech TalkAntivirus without the software
... Read more »
Athanasios Karantjias, & Nineta Polemi. (2010) Assessment of advanced cryptographic antiviral techniques. Int. J. Electronic Security and Digital Forensics, 3(1), 60-72. info:/
- March 24, 2010
- 06:32 AM
- 1,003 views
Web-Based Interaction: A Review of Three Important Human Factors
by Simon Harper in Thinking Out Loud
The main results from the analysis include that: (a) females have more disorientation problems than males; (b) flexible paths are more beneficial to experts while structured content is more useful to novices; and (c) Field Dependent and Field Independent users prefer to employ different search strategies.... Read more »
Chen, S., & Macredie, R. (2010) Web-based interaction: A review of three important human factors. International Journal of Information Management. DOI: 10.1016/j.ijinfomgt.2010.02.009
- March 24, 2010
- 01:01 AM
- 1,740 views
Tip of the Week: Genomicus and genome evolution
Today’s tip is on Genomicus. Genomicus is a great tool to visualize gene duplication, synteny and genome evolution. The search and display interfaces are quite straightforward, and there are lots of great features (viewing ancestral gene information, links out to resources, different views of phylogenies, etc) in the tool. This video is only a short introduction. You can delve deeper into the tool with the help and documentation, including an 11 minute video.
There is also a recent (advance access) paper in the journal “Bioinformatics” that will give you a lot more detail on how the database and tool works and what is there.
Muffato, M., Louis, A., Poisnel, C., & Roest Crollius, H. (2010). Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes Bioinformatics DOI: 10.1093/bioinformatics/btq079
You will also notice today the video is a SciVee embed. We are trying out a new way to post and share our tips. SciVee allows us to not only post on our blog, but for you to share the tip with others and also for scientists in the SciVee community to view the tips. This is only a test. We will be working with this for the next couple weeks to find the best way to post and share. Eventually, soon, we hope to share these on Facebook and Youtube also. If the video is not high enough quality for you (SciVee and other video sharing sites by necessity reduce size, you can try out the entire mpeg4 version a this link.
... Read more »
Muffato, M., Louis, A., Poisnel, C., & Roest Crollius, H. (2010) Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics. DOI: 10.1093/bioinformatics/btq079
- March 23, 2010
- 10:57 PM
- 490 views
The Dumbest Study I've Ever Read
by Neuropsych15 in The MacGuffin
This study has nothing to do with drugs, psychotherapy, or even neuroscience. It's about Jesus' head; more specifically, it's about Jesus' head in relation to the size of the main course in 52 different depictions of the Last Supper.I know what you're all thinking, it's barely past noon, and I've hit the scotch too hard this time. From the International Journal of Obesity:"Portion sizes of foods have been noticably increasing in recent years, but when did this trend begin? If art imitates life and if food portions have been generally increasing with time, we might expect this trend to be reflected in paintings that depict food. Perhaps the most commonly painted meal has been that of Jesus Christ's Last Supper, chronicled in the New Testament of the Bible. A CAD–CAM analysis of the relative food-to-head ratio in 52 representative paintings of the Last Supper showed that the relative sizes of the main dish, bread, and plates have linearly increased over the past millennium."First, it's spelled noticeably, not noticably. No need to thank me, I'm just here to help.Lead author, Brian Wansink, proudly displayed his virginity by saying, "I think people assume that increased serving sizes, or ‘portion distortion,’ is a recent phenomenon, but this research indicates that it’s a general trend for at least the last millennium."His brother Craig Wansink, proving that mental illness does run in their family added, "As the most famously depicted dinner of all time, the Last Supper is ideally suited for review."Here is a graph showing some of the data that will one day lead to a vaccination for jock itch. I am posting another graph below because I hate all of you. What they found was that "the main courses depicted in the paintings grew by 69%, plate size by 66%, and bread size by 23%" over the course of 1000 years. I've lost precious minutes from my life. I've created this post to waste your time as well. Be careful everyone. Stupid can kill...B Wansink and C S Wansink (2010). The largest Last Supper: depictions of food portions and plate size increased over the millennium International Journal of Obesity, 37... Read more »
B Wansink and C S Wansink. (2010) The largest Last Supper: depictions of food portions and plate size increased over the millennium. International Journal of Obesity. info:/
- March 20, 2010
- 11:10 PM
- 1,475 views
Using System-on-a-Chip hardware to speed up alignments
by Leonardo Martins in bioMCMC
In recent years there has been an explosion of parallel algorithms for solving bioinformatics problems, namely phylogenetic reconstruction and sequence alignment. These algorithms follow the growth of new hardware solutions like Field-Programmable Gate Arrays (integrated circuits capable of performing simple instructions in parallel), Cell microprocessors (like the one inside Playstation 3), Graphics Processing Units (nvidia [...]... Read more »
Galvez, S., Diaz, D., Hernandez, P., Esteban, F., Caballero, J., & Dorado, G. (2010) Next-generation bioinformatics: using many-core processor architecture to develop a web service for sequence alignment. Bioinformatics, 26(5), 683-686. DOI: 10.1093/bioinformatics/btq017
Manavski, S., & Valle, G. (2008) CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. BMC Bioinformatics, 9(Suppl 2). DOI: 10.1186/1471-2105-9-S2-S10
- March 20, 2010
- 01:20 PM
- 882 views
putting the processing pedal to the metal
by Greg Fish in weird things
Since the dawn of computers, the processing power of just about every computing device out there has been pushed ever upwards. Today’s mediocre laptops are faster than ten year old supercomputers and a modern supercomputer can carry out more than a quadrillion floating point operations per second, enough to take on complex problems in astrophysics, [...]... Read more »
Levitin, L., & Toffoli, T. (2009) Fundamental Limit on the Rate of Quantum Dynamics: The Unified Bound Is Tight. Physical Review Letters, 103(16). DOI: 10.1103/PhysRevLett.103.160502
Volkmar Putz, & Karl Svozil. (2010) Can a computer be "pushed" to perform faster-than-light?. n/a. arXiv: 1003.1238v2
- March 17, 2010
- 04:47 AM
- 1,021 views
Entre « effets de petit monde » et émiettement communautaire: la légitimation culturelle à l’heure de Facebook
by ---a in Bodyspacesociety.eu
par Antonio A. CASILLI (Centre Edgar-Morin, EHESS) [1]
Le texte qui suit a été présenté aux Journées d’études Les réseaux sociaux: Quoi de neuf ?, qui ont eu lieu à l’université de Toulouse II-Le Mirail, 16-17 mars 2010, dans le cadre des activités du Réseau Thématique 26 de l’Association Française de Sociologie.
La communication (ici en [...]... Read more »
Antonio A. Casilli . (2010) Légitimation intersubjective de la présence en ligne et formation de réseaux sociaux : Une approche ethno-computationnelle. II Journées d'études du RT 26 (Réseaux sociaux) de l'Association Française de Sociologie "Les réseaux sociaux: quoi de neuf ?", 16-17 mars, Université de Toulouse II - Le Mirail. info:/
- March 11, 2010
- 08:00 AM
- 668 views
Are you scummy froth or riding the business waves?
by David Bradley in Sciencetext
It’s perhaps an obvious statement perhaps needing only one word to qualify it – successful business sells. As an allegedly going concern, if you’re not selling your products or services, then you’re not likely to remain viable for very long. It seems to be too easy for companies to be distracted from this mantra by [...]Post from: David Bradley's Sciencetext Tech TalkAre you scummy froth or riding the business waves?
... Read more »
David Smallman. (2010) Without instructions or orders, there is no business. Int. J. Liability and Scientific Enquiry, 3(3), 179-182. info:/
- March 7, 2010
- 11:01 AM
- 908 views
The sociology of Chatroulette
by ---a in Bodyspacesociety.eu
by Antonio A. Casilli (Centre Edgar-Morin, Paris) [1]
By now, you might have heard about Chatroulette, if you are hip and tech-savvy if those two things at the sides of your face are your ears. By the way, I hope you did not click on the link. It’s not safe for work. And by that I [...]... Read more »
Peter M. Todd. (1997) Searching for the next best mate. In R. Conte, R. Hegselmann, and P. Terna (Eds.) Simulating social phenomena, Berlin: Springer-Verlag, 419-436. info:/
- March 3, 2010
- 08:00 AM
- 806 views
Hacking your online identity
by sciencebase in Sciencebase Science Blog
Geo-location services are very useful, helping you find a post office, ATM, decent restaurant, or hooking up with friends. They are commonly used in conjunction with smart phones and other mobile devices that ping your location (based on network coordinates or the global positioning system, GPS) back to the owner of a given system.
Location-based services [...]Hacking your online identity is a post from: Sciencebase Science Blog
... Read more »
T. Martin, C. Durbin, M. Pawlewski, & D. Parish. (2010) Future vision of identity. Int. J. Liability and Scientific Enquiry, 3(1/2), 86-98. info:/
- March 2, 2010
- 01:00 PM
- 836 views
Dawkins.net: Storm in a teacup 2.0?
by The Twenty-first floor in The Twenty-first floor
Anyone in the skeptical and atheist community who hasn't heard of the row that erupted over changes to richarddawkins.net forum probably still uses a 56K modem and a dialup connection.
This post summarises the fallout and explores the issue of online communities: are they real or illusory?... Read more »
Haythornwaite, C. (2008) Chapter 9: Social Networks and Community, Oxford handbook of internet psychology – Edited by Adam Joinson. British Journal of Educational Technology, 39(3), 561-562. DOI: 10.1111/j.1467-8535.2008.00855_4.x
- February 25, 2010
- 05:00 AM
- 1,280 views
Apache Maven: A Misbehavin’ Build Tool?
by Duncan Hull in O'Really?
One of the many tools we use in our team to manage the development of ChEBI software is an automated build tool called Apache Maven. Opinions are often divided on whether Maven is a good or a bad thing. Most of them are very subjective, argumentative and often very extended. See why does maven have [...]... Read more »
Stroustrup, B. (2010) Viewpoint: What should we teach new software developers? Why?. Communications of the ACM, 53(1), 40. DOI: 10.1145/1629175.1629192
Bjarne Stroustrup. (2007) Evolving a language in and for the real world: C 1991-2006. Proceedings of the third ACM SIGPLAN conference on History of programming languages. DOI: 10.1145/1238844.1238848
Bjarne Stroustrup. (1993) A history of C : 1979–1991. The second ACM SIGPLAN conference on History of programming languages. DOI: 10.1145/154766.155375
- February 24, 2010
- 08:00 AM
- 750 views
How to fix Wikipedia
by David Bradley in Sciencetext
The introduction of so-called Flagged Revisions on the infamous online information repository, Wikipedia, do not go far enough to allow the site to mature into an accurate and wholly verifiable Internet resource. Instead, the adoption of more traditional values is the only way forward, argue Australian information experts.
Wikipedia is a user-produced online encyclopedia and, since [...]Post from: David Bradley's Sciencetext Tech TalkHow to fix Wikipedia
... Read more »
Lichtenstein, S., & Parker, C. (2009) Wikipedia model for collective intelligence: a review of information quality. International Journal of Knowledge and Learning, 5(3/4), 254. DOI: 10.1504/IJKL.2009.031199
- February 22, 2010
- 02:02 AM
- 1,982 views
How Risky Are Social Networking Sites for Kids
by Dr Shock in Dr Shock MD PhD
This article discussed in this post, isn’t recent but the conclusion is very nuanced which isn’t always the case with publications especially in news media about social networking and kids or adolescents. Seems that politicians are advocating measures to restrict social networking for children in order to prevent assumed online sexual exploitation and Internet harassment.
Broad [...]
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Ybarra, M., & Mitchell, K. (2008) How Risky Are Social Networking Sites? A Comparison of Places Online Where Youth Sexual Solicitation and Harassment Occurs. PEDIATRICS, 121(2). DOI: 10.1542/peds.2007-0693
- February 20, 2010
- 02:10 PM
- 1,821 views
presenting the amazing evolving automatons
by Greg Fish in weird things
A while back I made a post about the use of robots to simulate evolutionary behaviors by giving them a kind of free reign and copying the programming of the machines most successful in their tasks into the rest of the test group to emulate natural selection. Now, the lead author of that study, Dario [...]... Read more »
Floreano, D., & Keller, L. (2010) Evolution of Adaptive Behaviour in Robots by Means of Darwinian Selection. PLoS Biology, 8(1). DOI: 10.1371/journal.pbio.1000292
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