MedWorm.com provides a medical RSS filtering service. Over 5000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Propeller Twist : RNA & Bioinformatics' source. Sat, 16 Aug 2008 14:46:39 +0100 http://fjossinet.u-strasbg.fr/blog/details?post_id=85 Tomorrow I will be at The new RNA frontiers symposium. The program looks very interesting with a special mention to the presentation of John Mattick titled “The human genome as an RNA machine”. John arrived today in our lab and it was a real pleasure to meet him for the first time. I will present a poster describing new features of the new S2S version that will be released in few weeks. The poster is available as a PDF file. Be careful, it’s a high-quality file (2,7Mb). (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=1012374 Wed, 07 Nov 2007 21:17:19 +0100 1012374 http://fjossinet.u-strasbg.fr/blog/details?post_id=83 I’m a big fan of the work of Ben Fry. He has great ideas about data visualisation, which should be (has to be?) a hot topic for bioinformatics in the next years (take a look at the cover of Nature about his visualization of the HapMap data). Ben is also the author of Processing, a great open source programming language and environment for people who want to program images, animation, and interactions. His new book about Processing has been released. He is writing another one for O’Reilly. Both are in my wish list. (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=959787 Thu, 18 Oct 2007 09:02:22 +0100 959787 http://fjossinet.u-strasbg.fr/blog/details?post_id=82 For those interested, you can download the poster presented by Thomas at the German Conference on Bioinformatics 2007 (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=925329 Wed, 03 Oct 2007 12:51:25 +0100 925329 http://fjossinet.u-strasbg.fr/blog/details?post_id=81 As explained in their MATHwire newsletter: “Wolfram Research is now the official math brain trust for the hit CBS series NUMB3RS.” The mathematical theories behind each episode are now explained on a dedicated website. It provides animations and interactive demos you can play within your Mathematica or by using the Wolfram Mathematica player (if you don’t have a license). Very interesting… (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=914124 Sat, 29 Sep 2007 14:41:52 +0100 914124 http://fjossinet.u-strasbg.fr/blog/details?post_id=80 The Science journal has just published the Science and Engineering Visualization Challenge 2007 results: “In the journal’s 28 September 2007 issue, Science, in partnership with the National Science Foundation, is pleased to present the winners and honorable mentions in the fifth annual Science and Engineering Visualization Challenge. The articles linked on this page describe the accomplishments of the creative and gifted scientists, artists, and others who put the winning entries together, as well as an online slide presentation that showcases the competition’s winners and honorable mentions.” Really beautiful… (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=909408 Fri, 28 Sep 2007 09:05:49 +0100 909408 http://fjossinet.u-strasbg.fr/blog/details?post_id=77 I have added to the wiki several screenshots of our graphical applications. (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=904560 Wed, 26 Sep 2007 07:09:34 +0100 904560 http://fjossinet.u-strasbg.fr/blog/details?post_id=76 3D Virtual Worlds could be the next big thing in e-learning and for scientific collaboration. Scientists have begun using such places to conference, teach, build and experiment. Second Life is one of the most popular of these worlds. The Nature Publishing Group owns an island named Second Nature where you can find living talks. On the Drexen Island other cool initiatives exist like the ability to make molecular docking : Among other nice places, you can also visit the Gene Pool, where Professor Max Chatnoir from Texas Wesleyan in Fort Worth, Texas, is teaching genetics: If you are interested to develop your own virtual world, I have discovered today the Croquet project: “Croquet is a powerful open, source software development environment for the creation and large-scale distributed deployment of multi-user virtual 3D applications and metaverses that are (1) persistent (2) deeply collaborative, (3) interconnected and (4) interoperable. The Croquet architecture supports synchronous communication, collaboration, resource sharing and computation among large numbers of users on multiple platforms and multiple devices.” The Croquet SDK is written with Squeak. My next programming language? ;) (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=885390 Wed, 19 Sep 2007 22:17:50 +0100 885390 http://fjossinet.u-strasbg.fr/blog/details?post_id=75 All the rss feeds of my blog are now accessible through FeedBurner. By the way, I have also created new feeds to be warned about the S2S, Assemble and PARADISE posts. Please use the new rss links to let me see the average number of subscribers I have. Thanx ;) (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=885391 Wed, 19 Sep 2007 20:23:13 +0100 885391 http://fjossinet.u-strasbg.fr/blog/details?post_id=74 It is well known that a developer should learn at least one new programming language every year, especially if the language of choice proposes new programming paradigms. My LotY 2008 could be Scala or Erlang. If I have enough time of course ;) Any information about the use of these languages in bioinformatics ? (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=874627 Sat, 15 Sep 2007 15:10:56 +0100 874627 http://fjossinet.u-strasbg.fr/blog/details?post_id=73 Reading DZone, I have discovered two news pointing to some attempts to rewrite the python examples of the book using Ruby and Common Lisp. (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=874628 Sat, 15 Sep 2007 14:47:16 +0100 874628 http://fjossinet.u-strasbg.fr/blog/details?post_id=72 It’s new and it’s under heavy construction. It describes the PARADISE framework and the upcoming new versions of S2S and Assemble. As explained in the first page, PARADISE, S2S and Assemble will be hosted by the SimTk website. The old versions of S2S and Assemble are still available at bioinformatics.org. More to come… (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=874629 Sat, 15 Sep 2007 14:33:33 +0100 874629 http://fjossinet.u-strasbg.fr/blog/details?post_id=71 I have discovered recently Saaien Tist, a very interesting blog maintained by Jan Aerts. Jan has released recently a Ruby API for the Ensembl database. This library uses ActiveRecord, the famous ORM provided by Rails. Beside the fact that this is a very good news for the Ruby language, and since the Ensembl team has recently left behind their Java APIs, this new library is also a good opportunity for Java developers once coupled to JRuby. (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=863780 Tue, 11 Sep 2007 21:27:51 +0100 863780 http://fjossinet.u-strasbg.fr/blog/details?post_id=70 During this august, the O’Reilly publisher has released an interesting book named Programming Collective Intelligence. “This fascinating book demonstrates how you can build web applications to mine the enormous amount of data created by people on the Internet. With the sophisticated algorithms in this book, you can write smart programs to access interesting datasets from other web sites, collect data from users of your own applications, and analyze and understand the data once you’ve found it.” The author, Toby Segaran is a software developer and manager at Genstruct, a computational systems biology company. I have readen recently some papers published by this company. The publication on their Causal Modeling is very interesting: “It is through the creation of a computer aided framework for human understanding that we can begin to comprehend how these collections of molecules act as integrated biological systems, and to utilize this knownledge to rationally engineer the future of science and medicine” I have added this book to my Safari bookshelf. (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=858385 Mon, 10 Sep 2007 21:52:29 +0100 858385 http://fjossinet.u-strasbg.fr/newsdetails/index/62 P.A.R.A.DIS.E. stands for "Platform to Analyse RNA Data over a DIStributed Environment". It will federate the S2S and Assemble projects. More to come.... (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=486408 Tue, 31 Oct 2006 07:36:47 +0100 486408 http://fjossinet.u-strasbg.fr/newsdetails/index/61 I have just read that Charles Nutter and Thomas Enebo, two core developers from the JRuby project, will become employees at Sun Microsystems this month. And they will work on JRuby full-time. This means that the development of a "whole-platform" Ruby-on-JVM is an official strategy for Sun. This is really a great news. Ruby and bioinformatics Java libraries are closer than ever before. (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=486409 Thu, 07 Sep 2006 19:02:29 +0100 486409 http://fjossinet.u-strasbg.fr/newsdetails/index/60 Since the hype around the rails framework, we can read many posts in the blogosphere comparing python and ruby. Ruby is a great language and I think that features like Drb or its ability to develop easily domain-specific languages (DSLs) can help to design new bioinformatics killer apps. It seems that an other advantage of Ruby (over Python) is the brillant marketing arount it. It's funny to see how the ugly Python homepage has changed under the recent pressure of the Ruby community (and Ruby strikes back recently ). But I have the same feeling as the one described in this recent post. Ruby is too much attached to the Rails project. I underlined this problem recently. Rails is a Ruby DSL for web development. Learning Rails is like learning a new language. I think that the hype around Rails attract new Rails developers and not new Ruby developers. This is a big difference!! I'm afraid that all the upcoming Ruby projects will be tightly linked to the Rails framework. In bioinformatics, the main goal is the biological discovery. You need to be productive as quickly as possible. And being productive in bioinformatics means to easily parse heterogeneous biological formats, display and manipulate biological data with 2D and 3D rendering, extract automatically biological knowledge using different algorithms (HMMs, neural networks, k-nearest neighbors, SVMs, semantic reasoner, ....). Python can provide such libraries now. Ruby cannot (except BioRuby). Today, Python is the best compromise between funny (web2.0) and less funny (science) stuffs. Since Mathematics Is Biology's Next Microscope, languages like R, Matlab or Mathematica are good candidates too. Using them, we are very far from the hype and marketing but closer to the biological discovery. (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=486410 Sat, 26 Aug 2006 06:13:03 +0100 486410 http://fjossinet.u-strasbg.fr/newsdetails/index/58 The current CTWatch Quaterly issue is focused on the "Trends and Tools in Bioinformatics and Computational Biology" (thank you Yann for the link). By the way, I have seen on their blog an interesting post on the Semantic Grid. (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=486411 Tue, 22 Aug 2006 16:39:55 +0100 486411 http://fjossinet.u-strasbg.fr/newsdetails/index/57 During the last months, we have released a new java tool named Assemble. It has been entirely written by Thomas Ludwig, a PhD student working with me. Assemble is an extensive rewriting of a previous tool named MANIP. During the last years, MANIP has been intensively used in my lab to construct RNA 3D models for RNA molecules with unresolved tertiary structure (take a look at these publications for more details). Recent progresses made in the genomic area allow to sequence new genomes in a reasonable amount of time, which leads to the discovery of new RNA families or to the accumulation of new orthologous sequences. Despite the fact that the resolution of RNA tertiary structures has increased dramatically in the last years, these structures are unresolved for the large majority of RNA molecules discovered so far. Consequently, the availability of tools able to improve the construction of RNA 3D models is necessary (at least for us ;)). The construction of a 3D model is an iterative task where the user needs to confront all informations available for the corresponding RNA molecule. To resume, we can identify several steps during the construction process. The first step needs the identification of the regular helices within the RNA sequence. This leads to the definition of a secondary structure. There are several ways to identify such helices. If you have only one sequence, a tool like mfold can help you. RNA scientists know that one of the most valuable strategy is the construction of a multiple-alignment. If you have several orthologous RNA sequences within an RNA family, you can try to search for covariations allowing to easily define the locations of the regular helices. Whatever your strategy, once you have a secondary structure for your RNA sequence, Assemble allows you to import and to edit it (if necessary). You can also construct a secondary structure directly from scratch. Then, Assemble generates a first draft for the RNA 3D model. The next step in the construction process is focused on the single-strand regions (hairpin and internal loops, bulges and multiple junctions). At now, Assemble is not able to identify a "structural pattern" within such regions to automatically fold them. Implementing such ability needs more experimental results. At now, the user has to confront informations from different kind of experiments (multiple alignment, chemical probing, mutagenesis,...) to deduce a folding for a 3D region. Moreover, the "modeller" needs to master the current RNA structural knowledge. Indeed, we know that the RNA 3D structures are constructed with recurrent motifs (named RNA tertiary motifs). Consequently, the modeller has to determine if a set of experimental results for a 3D region is compatible with the features of a given tertiary motif. Assemble provides a widget to browse an embedded RNA tertiary motifs repository. This widget displays all the informations for a given motif already observed at high resolution and allows to easily fold a 3D region according to it. As described above, a multiple-alignment is one of the most valuable tool to construct a 3D model. It contains the "history" of the RNA family. It reveals how the 3D structure has evolved with the constraint to conserve the original biological function. Consequently, we want to link Assemble to a multiple-alignment editor. The S2S framework provides such a tool (named RNAlign). The interconnection between S2S and Assemble will be the next step of our work and the topic of an upcoming post. (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=486412 Tue, 08 Aug 2006 08:18:31 +0100 486412 http://fjossinet.u-strasbg.fr/newsdetails/index/56 After several months without any post, I have decided to restart this activity. Starting from now, I will talk more about the tools I try to develop and the reflexions around them. Propeller Twist is up since one year now, and I have decided to redesign it. I have moved the links and publications references to my del.icio.us account. So, plenty of good news except that I'm not living in an happy country. (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=486413 Thu, 03 Aug 2006 12:51:12 +0100 486413 http://fjossinet.u-strasbg.fr/newsdetails/index/53 On Monday the 13th, I went to the sbiolbd2006 seminar day organised at the EPFL in Lausanne, Switzerland. It was my first event focused on ontologies. Among other people, i was very pleased to meet Eric Jain who manage the UniProt RDF project and to eat and discuss with Robert Stevens from the Manchester University. Robert has presented a work I have searched since I read ontology papers : how to use ontologies to automatically annotate new sequences? His team has transcribed as OWL-DL rules what the scientists know about the conditions needed (and sufficient) for a protein to be a member of the phosphatase family. With few classes and a lot of protein instances stored in their instance store database, they have constructed a tool able to make the reasoning. At the end of the day, we have discussed about the challenges for ontologies. Data providers cannot only annotate their data using ontologies and let the biologists find the optimal queries to discover new knowledge. Ontologies should help the construction of tools allowing biologists to ask simple/easy queries and to get complex answers. Consequently, the knowledge described in an ontology should be represented as comprehensively as possible AND be reasoned with as effectively as possible. (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=486414 Fri, 24 Feb 2006 16:54:01 +0100 486414 http://fjossinet.u-strasbg.fr/newsdetails/index/54 I have just opened the survey to see what people think about a social bookmarking tool for the RNA Society. To answer quickly to Enro's comment, the idea is not to reinvent the wheel. I think that, like ontologies, each scientific community should have its own tool. To give an example, it's difficult to use general bookmarking tools to see what is hot/popular within the RNA community. It's flooded with the popular items registered by all the other communities. Moreover, in a second step, my idea is to create new tools using this RNA knowledge database. As you can imagine, I want to use semantic-web and web2.0 technologies to produce them. (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=486415 Tue, 21 Feb 2006 08:35:46 +0100 486415 http://fjossinet.u-strasbg.fr/newsdetails/index/52 Nine proceedings are available here. A must read !! (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=486416 Sun, 29 Jan 2006 09:45:21 +0100 486416 http://fjossinet.u-strasbg.fr/newsdetails/index/51 Recently, i have discovered this one. Does anybody have informations about it ? Looking at the table of contents, i'm curious about the Bayesian Web chapter. I think i will order it. (Source: Propeller Twist : RNA & Bioinformatics) Propeller Twist : RNA & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=486417 Sat, 21 Jan 2006 08:47:11 +0100 486417