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2009 in bioinformatics science 2 0 in poland getting popular recognized as important 28 nov few days ago i had a chance to speak about science 2 0 at the institute of biochemistry and biophysics of polish academy of sciences the one i m affiliated with compared to the seminar on the same topic i gave at the same place but for much smaller audience 4 years ago i had much more stories to tell way more real life examples and better idea of where the whole 2 0 meme is leading us i also got better at speaking 4 years ago some of my colleagues literally slept on my seminar so message got clearer and messenger had improved but given wide interest in the topic from inside and outside of academic environment already before the seminar i think two things had happened in poland in the last 4 years first internet got recognized as a game changing technology and people simply are interested in any new way they can use this tool yes i know it s 2009 if you live on the nets it s hard to realize how slow adoption rate is outside of virtual world s second thing is that internet as a tool is also recognized as important for example people had ideas to include science 2 0 topics into program of phd studies i will follow up on this topic in a week or two getting popular important only wide adoption is what we need comments off on science 2 0 in poland getting popular recognized as important posted by pawel szczesny on november 28 2009 in bioinformatics notes from next generation sequencing workshop in rome 21 nov i was in rome for two days attending next generation sequencing workshop organized by embrace eu fp6 noe uppmax and caspur with the support of the italian society of bioinformatics it was pretty interesting event and i want to share with you couple of interesting things i ve learned there hardware layer first day was devoted mainly to the hardware side of ngs it started with a presentation from tony cox from sanger institute who described a hardware setup used to support their sequencing projects at 400 gigabases a week current output sanger it infrastructure is stretched in every direction capacity availability redundancy and tony pointed out that each sequencing laboratory is going to face similar issues did sooner or later his advice for such labs was to estimate first number of bases produced and then use multipliers to assess storage requirements for the project a minor thing that i ve noticed in his talk was exposing databases as filesystem via fuse layer i might use that approach in some projects too george magklaras from the biotechnology centre of oslo described a number of approaches they took during implementation of their infrastructure he talked about fcoe fibre channel over ethernet and pointed out that it s cheaper and almost as efficient as fibre channel alone at the centre they use lustre sanger is too high performance networked file system but they benchmark other solutions too because some situations projects require transparent and efficient data encryption mostly medical data similarly to tony george pointed out that compartmentalization of data is necessary as moving large amounts of files over the network creates a unnecessary bottleneck other interesting talk was from guy cochrane from ebi about sequence read archive it was an overview of the project but again with few interesting tidbits that drawn my attention one of them was aspera much faster alternative and secure at the same time to good old ftp he also presented a data reduction strategy that if i understood correctly is not yet implemented over at sra but might be some day in the future first point was deletion of intensity data that s something perfectly reasonable but is heavily opposed by a number of scientists then all only consensus is preserved plus second most frequent base important for polymorphism studies the minimum for long term storage was proposed to consist only of sequence and quality data software majority of second day was devoted to software it doesn t make sense to list all described projects i will share with you only my general impression despite large number of scientists devoting their time to develop new tools for next generation sequencing data i think that software lags a little behind other technological advances in this area in case of really large amount of data assembly becomes hard or impossible mapping erroneous annotation too slow pilot study of 1000 genomes project generated so much data that computing farm was busy for full 60 days on single cpu it would take 25 000 days software development for ngs differs dramatically compared to scientific software in general and needs much much better programmers than we usually are for example desmond higgins was praising open source software they found extremely fast implementation of upgma algorithm much faster then their own and they could speed up their tool seedmap so much that it s running it on even largest family of sequences in a reasonable time another bottleneck was data presentation layer there are some attempts to make digging into data easier but having a biologically meaningful overview is as hard as it was before other people pointed our that problem too i wasn t the only biologist there need for stronger community probably the most funny part of the workshop was the discussion about creating an organized community of people working with next generation sequencing technologies it was funny is this sense that some consensus about community emerged quite fast how to build it that was another story obviously lots of participants were sure that if they build a site people will come yeah sure i ve suggested using wiki in the first place and additionally hire a community manager if they really want to gather people from many different forums sites groups etc lot s of people didn t buy these ideas suggesting more traditional approach so curious if they were right i m going to follow development of this community ngs high tech probably the most important lesson was to realize that sequencing is a field with very high requirements for infrastructure and even higher requirements for skilled staff basically every element of the infrastructure may become a bottleneck and if you want to avoid it cost of data maintenance and analysis exceeds very fast cost of producing the data when i talked about it to many people during the last year i m involved in some sequencing projects at the analysis annotation step often people felt i overestimate infrastructure needs now i have some specific number to back it up 2 comments posted by pawel szczesny on november 21 2009 in bioinformatics tags next generation sequencing ngs workshop microstocks are for scientists too 05 nov money is rarely directly discussed on science blogs but rarely science bloggers say that they don t care quite a number of them run advertisement or affiliate programs on their sites trying to monetize the traffic they generate and while i don t know specific numbers my estimate is some time ago i did run such programs on a photography blog which was way more popular that this one that in majority of cases it buys them a coffee or two per week this blog is hosted over at wordpress com and wp com team forbids inserting your own scripts into the blog occasional affiliate links seem to be fine if you re interested making money from google ads wasn t an option for me but i have tried to earn money by sending images of molecules to microstock sites and that seems to be more profitable than previous strategy inspiration to write this post came from the fact that i ve recently logged into one of the sites and i was quite surprised to see that despite the fact i didn t upload anything for almost two years my images are still selling quite well in majority of microstock sites your gallery exposure is bigger if you upload new stuff on regular basis so the conclusion is that after two years there s still not many similar images of molecules to choose from above you can see one of the attempts to create nice picture of hemoglobin molecule that should give you an idea what images are selling well simple clean bright colours etc few other suggestions pay attention to the license under which the software you use to generate images is distributed for example you cannot use vmd or chimera both have non commercial licenses while qutemol under gpl is fine use automated submitters available for all platforms instead of relying on ftp you just don t want to manually annotate dozens of images on the web the other route is to fill ipct tags submit to all microstock sites that let you in but start with the bigger ones istockphoto dreamstime fotolia shutterstock etc if you have time experiment with graphics or 3d software additional modifications in gimp or blender occasionally produce interesting images if you live in a strange country check first regulations under which you can earn money via microstock in poland for example you need to start a company first which as my polish readers can confirm is a really painful process 2 comments posted by pawel szczesny on november 5 2009 in money tags gnu general public license microstock photography wordpress com basket as a writing tool scan as a collector 03 nov basket has been my favourite notetaking software for a long time until i had switched to mindmaps quite recently i ve discovered another use for it a writing aid basket in one column mode allows to rearrange your notes just by dragging them up or down there re keyboard shortcuts for that as well when i m writing a longer piece i don t need to hold a structure of the article in my head i just collect all the pieces quotes blog posts fragments my own notes links tweets etc and then rearrange it as much as it s needed when the flow of the thoughts is optimal i start to connect these pieces by writing some text in between i don t have devonthink i don t have mac but for finding similar things in my archive i use scan scan can aggregate content from a number of sources it has plugins to read pdfs openoffice and msoffice files or even rss feeds analyze it automatically assign tags extract metadata etc it has lucene engine built in and does quite a good job of finding related pieces in the archive it s quite buggy doesn t read all pdfs such as encrypted metadata extraction doesn t work as expected but overall the tool has a potential and there s no similar program available on linux platform anyway its development was recently restarted so there s hope it s going to be improved in a near future additionally it has a nice eye candy a visual overview of relations between tags this strategy is similar to the workflow described by steven johnson but without devonthink so far i haven t found anything better under linux but probably i need to check online apps things do change every month 1 comment posted by pawel szczesny on november 3 2009 in research software tags basket metadata rss scan workflow transitions transitions 28 oct quite a few things happened while i was away if you re interested here s not so short summary of my internet hiatus research area i think i m done with bioinformatics my current research area seems to be located somewhere between systems biology theoretical biology and information complex systems theory i hope to build on dawkins work deal with emergence in biology and study subtle effects in biological systems while i m not sure if i will have anything interesting to show ever i don t have energy to do yet another project which involves programming web interfaces dealing with data annotations modelling etc i m done with analytics time for synthesis carrer last year i wrote a post dreaming about small non profit contract research organisation this model of research as a service has materialized in a virtual research institute which we have finally launched few days ago materialized in something virtual sign of times the setup is quite simple the institute gets a project or applies for such and then it searches for researchers institutions freelancers which are willing to subcontract parts of the project we have outsourced not only research part even money gathering writing grants etc is done by external company the setup is quite flexible and pretty transparent for example we may represent somebody s rights but no intellectual property is owned by the institute why such institution we become a single point of contact for a large and diverse group of scientists which are willing to do some research for real money but don t have time and energy to hunt for gigs by themselves while i have an academic job i m in the middle of transition from being a freelancer to being a jobs provider for freelance scientists more on that in some other post open science i plan to spend way more time on advocating open science all of its flavors but in polish this step is out of large frustration that even prominent figures in polish science have no idea about changes in the science internet aware researchers are watching and creating knowledge about even basic things like open access is dramatically low in poland a number of people here equals oa with low quality publications which have not been peer reviewed with few friends we have a number of projects in the pipeline for example we hope to launch a nation wide created by professionals promotional campaign bilboards tv commercials etc for open science if any of these actually works i will let you know if we have any measureable success labels labels robert anton wilson tells a nice story in his book prometheus rising william james father of american psychology tells of meeting an old lady who told him the earth rested on the back of a huge turtle but my dear lady professor james asked as politely aspossible what holds up the turtle ah she said that s easy he is standing on the back of another turtle oh i see said professor james still being polite but would you be so good as to tell me what holds up the second turtle it s no use professor said the old lady realizing he was trying to lead her into a logical trap it s turtles turtles turtles all the way another story is a comment from my advisor about putting my real research plans in some proposal he supports these plans the most likely a reaction from reviewers will be something like this nice start some decent papers phd looks good and then he got crazy i feel like screaming labels labels labels all the way when facing stiff schemas of what scientists is or what artists is etc it s a hard task by itself to integrate multiple passions and multiple interests into a coherent structure i don t need another set of issues because of labels people attach to seemingly creative professions but limiting myself only to topics consistent with the image of an online scientist became even more frustrating therefore expect that this blog or any other venue i choose to express myself is going to become a lot more diverse in topics and form 1 comm...