shit Neil, stay out of his shit, man! Back off! ;-) - PauloNuin
It's worth reading past the cussing and overblown style with PP; he's pretty sharp. The reaction he displays here is the least we happy-hippy Open Everything types can expect from (I guess) a majority of established researchers. In a lot of cases there won't be a thoughtful argument (which you can get out of PP), just reflexive rejection of anything new and potentially risky. - Bill Hooker
And once again, the tired old arguments about scooping and "if you worked in a competitive field" in the comments. I firmly believe that when most people say they were "scooped" all they mean is "someone else published first", rather than "someone stole my data". In competitive fields with lots of people working on the same thing, the odds that the smarter/bigger/better-funded lab will beat you to it are rather high. It's rarely anything to do with them stealing your results. - Neil Saunders
Further to Neil's point: when people say "scooped" and mean "got there first", does it not occur to them that the best way out from under competition with bigger, better-funded labs is to promote collaboration? Yeesh. - Bill Hooker
I have another issue with Open Notebooks, and I'll blog about it when I have time. (Not now) I took some pictures of my paper notebooks to show why it works so well on paper and I can't possibly see how that could ever be done online with the same meticulousness and efficiency. - Eva
Eva ... there is one big reason software will beat paper. Search and eventually, regulation. You need a traceable database. That's very very important over a period of time, even if it doesn't make a difference at an individual level (this is separate from the open discussion) - Deepak
Did I hear an "argument from personal incredulity" ? No-one is suggesting wresting the paper notebook from the (cold, dead) hands of die-hard bench scientists. It's about the advantages of digital data, as Deepak said. - Neil Saunders
I think open notebooks are a very good idea. The rawer the presentation, the less good stuff gets left out. And to quote from the comments: "Not This "Blogging" Shit Again! People are still going on about the completely absurd idea of "blogging" their polemic and publishing it on the Web? Who the fuck wants to read someone else's half-completed thoughts and uninformed arguments?" - j1m
but how am I supposed to convert my pictures and arrows across the page into anything digital? Scan? When? I am already usually a week behind in actually copying notes and drawings I scribbled on tissue paper in the cell culture room in my actual notebook. I just don't understand. Show me a cell biology Open Notebook. Where are the blot pictures? - Eva
Also, I'm not at all a die-hard bench scientist. The die-hard bench scientists are rarely online. They are in labs with 5 people per computer, and they only use it to check e-mail twice a day. I'm the "computer expert" in my lab, because I know how to plug the network cable back in when "the internet is broken on just one computer". These are the people I'm concerned about. They are not opposed to sharing their data, but they're opposed to using the 'net for new things. - Eva
I'm pretty die hard bench scientist but I'm not scared of computers. Eva, it is fair to say that there aren't very many very good electronic lab notebook systems around. I can say this because I'm involved in developing them. But there are some adequate systems around - and we use ours for molecular biology and protein characterisation (grow E. coli, make protein, modify gene, etc). So we have the ability to upload pictures - also the ability to scribble on them but we would love to have more features - Cameron Neylon
But the paper argument is a bit empty in my view. You can always take an image, draw on it and scan it. You can even have a one button scanner that goes straight to your lab book if you want. Think of it from the perspective of someone ten years from now: 'How did you ever manage with out having searchable video in your lab book? How did you ever do cell biology without that?'. The tools will come - and at some point the electronic will be better. I agree we're not there yet. - Cameron Neylon
Can I just add 'Not this physioprof flying off the handle every time someone says "open" shit again'...and yes I know he/she says useful stuff that I often agree with but I really don't get what the bee in the bonnet is about this. Not like we're forcing people to do this - just saying that we think there are reasons why its good. - Cameron Neylon
This blog post would be more interesting if it contained much beyond ad-hominem and straw men. To me this attitude is part of a larger problem I see a lot these days - someone floats a moderately raw idea out for consideration, and armchair commentators lambast the flaws and declare it will never work, as opposed to constructively working to address the issues that they have. - Jason Winget
I don't even mind the straw man - I just wish PP would move on from the same argument that we've been through several times before. Obviously this is a smart and savvy person and just recycling the same objection seems a bit lame really. - Cameron Neylon
All good points by Cameron. I would add that labs with 5 people/computer should perhaps be worried in this digital age and taking steps to rectify matters. It bears repeating: we're not saying that the only notebook is the digital notebook and we're not saying that digital = open. We're just floating ideas that we think are useful and one day, could be the norm. - Neil Saunders
And the answer to "how do I digitise the doodles in my lab book" is obviously, you don't. You have to think outside of current practice and imagine what tomorrow's will be - or what you'd like it to be. If the answer is paper, that's just fine. Ultimately though - is that solution archivable, searchable, easy to analyse at a later date - by you, never mind anyone else. - Neil Saunders
And finally (!) - one day, lab equipment will take notes for us. See Cameron's blog for posts on that exciting topic. - Neil Saunders
Eva - a good example of something you can do on an online notebook is interactively link to raw data. For example if you click on any of the NMR links on this page you can then left click and drag to zoom into any region of the spectrum: http://usefulchem.wikispaces.c... - Jean-Claude Bradley
I usually just say it is a type of Partial Open Notebook Science - Jean-Claude Bradley
I still don't believe in scooping :) - Neil Saunders
I think delayed notebooks wouldn't prevent scooping, considering that scooping in notebooks is even an issue. - Ricardo Vidal
I am with Neil .. and after this weeks workshop even more frustrated - Deepak
I put in my more than two cents on this thread. I think the jury is out on which model works for which scientific field until more people from more fields try it out. So far there are a couple physicists, chemists, one molecular embryologist :-) and perhaps some biostatisticians? but we need larger sample sizes and more representativity. Where are the astronomers, the mathematicians (presuming they even keep lab notebooks), the geneticists, the cell biologists...? - Heather
How long does it take comments to come up at Scienceblogs? I made two some five hours ago... maybe the moderators are still in bed or something. Grumble. - Heather
Can anyone point to an example of scooping? I don't think it happens nearly as much as people think, and as you all know, proper ONS uses timestamps anyways, right? - Mr. Gunn
@Mr Gunn: I can give you one example of an attempt, when a certain Prof Scumbag found out from my PhD supervisor what I was working on, he put a postdoc on the same question. Happily I knew the postdoc, and he just kept "oh, I haven't got to that" until I'd published! Note that I have no proof, you'd have to take my word for this. Similarly, stories abound: I don't think I've met a PI who didn't have a story of someone throwing together a sloppy paper to scoop their conference presentation. - Bill Hooker
...cont'd: Very seldom does anyone take actual action. All I did, after all, was sabotage the attempt: I didn't make a formal complaint. We all know why I didn't, but that doesn't make it right. I have only one example where action was taken: this paper (http://www.pubmedcentral.nih.g...) contains this addendum (http://www.pubmedcentral.nih.g...) only because a senior scientist complained to journal editors and so on. - Bill Hooker
...cont'd: For instance, I could point to a paper which contains a bunch of crap (I can vouch for this) because it was slapped together after A saw B's presentation at a conference (I can't verify this -- which is why I won't point to it). My point, and at long last I do have one, is that timestamps are only half the answer. The other half is a willingness to follow up, assuming good faith error but willing to lay on the hurt if there really is a bad actor involved. - Bill Hooker
I've heard about people slapping together papers after seeing a conference presentation, and conceivably one could do the same after seeing an online presentation about research too. Now the question is whether such slapped together papers end up in better journals and cited more than the more complete research reports. If the slapping together is done by a more well-known lab, I can certainly see this being a problem, but I can also see well known successful labs being less likely to be bad actors. - Mr. Gunn
"whether such slapped together papers end up in better journals and cited more" I think they usually do, because the culture places such a premium on being first. - Bill Hooker
Short-term, maybe, but long term, like over 10 years, would the sloppy paper be expected to have the most cites? Want to find some crap papers from 1998 and do a quick experiment to see? - Mr. Gunn
I'm always in favor of finding out by experiment, but I don't have time for that one right now... Thinking more about it, I would expect the sloppy papers to have a shorter half-life just as you indicate. Problem is, science is self-correcting on a long timescale, but grant/hire/tenure decisions aren't. I do like your proposed expt; maybe put it on a BioGang backburner and let it simmer a while? - Bill Hooker
I would add it to the wiki, but it seems that my registration has yet to be approved... - Mr. Gunn
Mr. Gunn when did you apply for an account at OWW? - Ricardo Vidal
I think it means that bloggers get access to papers before publication like science journalists do, provided they don't break the news before the official release? Can someone clarify? - Neil Saunders
They have done that unofficially in the past, so looks like they are formalizing part of that process - Deepak
@Neil Yeah, you can't blog about it until after the embargo date has passed. - Euan
This is great. Levels the field for bloggers wanting to work as science journalists. - Pedro Beltrao
"Bloggers wishing to apply for inclusion in our press list should do so through our contact form including links to 6 blog postings written by them in the last 6 months discussing the content of primary research papers. " - Mr. Gunn
Very cool! Thanks for the heads up :) - Ricardo Vidal
Yes, it is already happening to some degree. I'm a blogger and PLoS sends me the same email announcing upcoming papers that they send to professional journalists. Often times they attach the real deal PDF to the article. - Kambiz Kamrani
THe dissemination problem - need to share resources versus protectionism. Disclosure through journals does not work. Disseminating _claims_ not datasets. Limited metadata. BUT disclosure through repositories is not rewarded, threaterns future research (resource requirement) is labour intensive, conditions are not clear (formats, standards, IP, raw v processed, pre or post publication how to check quality etc etc etc) - Cameron Neylon
Solution - disclosure policies? shift in the reward system? ADV: encourage disclosure, enforce formats, value _all_ existing forms of contribution to research. DISADVANTAGES: secrecy concerns, enforcement? radical shift from competitiveness to collaboration (need to reward data donation - How?) - p.s. it has worked in arabadopsis - Cameron Neylon
The classification problem - stability of categories veeruss dynanism and diversity of research practice. Can classifcation enable collaborative ressarch without stifling development and innovation? - Cameron Neylon
Solution? Bioontologies ADV: controlled vocab, dynamic system can be updated (if well curated), parameters flexible to user needs and competences DISADVANTAGES: manual curation, what constitutes 'best available knowledge' need to institutionalise dialogue between curators and users - Cameron Neylon
A common theme that comes up seems to be the need for high trained people to manage curation of data and/or description. Which relates back to rewards again. - Cameron Neylon
Suggestion that biologists and ontologists have different mental models and that is partly the problem. Biologists argue from a specific case, ontologists want to build the general case. Example that the potential for forking is built into Wikiproteins - Cameron Neylon
'institutionalising dialogue' means providing a framework for making sure the discussion goes in both directions from users to curators and vice versa. Create feedback loops, controlling at journal submission (submission to TAIR is a requirement for publication in Plant Physiology). Ontologists are bloggers! But are the users? Training workshops etc - Cameron Neylon
Dialogue between users, funders, and db curators needs to be insitutionalised (have institutions assocaited) and need to be enforced - Cameron Neylon
GOing into breakout group on 'incentivising data sharing' any comments anyone wants to drop into that? - Cameron Neylon
Just 2 things, Cameron. There's positive incentives, such as increased visibility, but another incentive is simply removal of obstacles. Tying into "having trained data curators available" so bench scientists don't have to learn scripting and markup! - Mr. Gunn
Sorry, didn't get this until after session had finished - visibility was brought up, and a lot of discussion about obstacles but I don't think there were any radically new ideas on what to actually do about it - Cameron Neylon
work options, grad school options, moving to US options... - Ricardo Vidal
those are all GOOD options, you don't have bad ones ... - PauloNuin
within each option, I need to find opportunities and assess requirements - Ricardo Vidal
I was in the same situation some months ago. IMHO it's better to have more options than none Good luck and let me know if I can help - PauloNuin
Don't get too analytical on it though. As people have said, all good problems to have - Deepak
Yeh, good luck. And remember that when you look back you will realise it was the random choices that you didn't notice at the time that make the real big differences. Or to put it another way - don't sweat it too much, go with your gut feeling, and never spend too much time on 'what ifs' - Cameron Neylon
Take the 2-3 topics of general interest, wash them thoroughly, until completely free of criticism and discussion. We recommend today 'Dark Energy', 'Quantum Gravity', and 'Large Hadron Collider', or whatever this week's special offer of your local blog scene is. Unwrap the prepared frequently used words, and carefully check whether some have become stale over night.
In a large, non-stick pan, warm the topics of general interest over medium heat. Add the frequently used words and cook until thickened to less than 10 sentences. Add ½ cup of superlatives and mash them with the back of a wooden spoon. Gradually stir in the parameters and simmer together for 4 to 5 minutes. - Duncan Hull
Confirmed. Because of larger social networks, I guess... - Egon Willighagen
seems related with domain expertise, your own institution only knows so much, the sweet spot is about 5 collaborators. It was a great talk, the work is under review at the moment, hopefully it will be out soon. I'm going to blog up the talk later when I get a chance. - Ian Mulvany
This lines up in my mind with Andy Powell's talk I saw at Talis a few weeks back where he pointed out that 'the institution' really lines up with real social or collaborative networks - Cameron Neylon
Correlations are a way of catching a scientist's attention, but the models and mechanisms that explain them are how we make the predictions that not only advance science, but generate practical applications. - Richard Akerman
lots of things scientists don't get credit for - Cameron Neylon
Including data in the RAE- or in metric based systems? - Cameron Neylon
what is the incentive? What is the problem we are trying to address? - Cameron Neylon
One solution is the 'data' paper to go along with the 'tool' paper - Cameron Neylon
special journal issue highlighting the products of shared data suggested - Cameron Neylon
peer to peer sharing: infrastructure issuesm, woried about security, but potential for shairng is high - Cameron Neylon
IP issues: disciplinary differences - social science data has limited re-use possibilities. Who owns the data, or the sample, or the genome. Privacy issues. Diffferences in the types of question that benefit from sharing. Some questions much better suited to being answered with shared data. Rights of subjects to be involved in governance of results, data, exploitation. - Cameron Neylon
Data Standards: Necessarily a two way street - Cameron Neylon
How well are things working? Tower of babel analogy, many formats, vocabulariesm few standards. WHy do we care? Data exchange, comprehensibility of work, scope for re-use. Public funding- public data - Cameron Neylon
What does a standards body need? Requirements, formats, vocabulary. Regular full blown open meetings, mailing lists etc. Some sense of why and what is being done. Testing is important, but difficult to get people to do. Uptake by all various kinds of stakeholders is is crucial (e.g. MS instrument makers), journals setting a bar, the user community - Cameron Neylon
'I don't drive my car by reaching into the engine' - What does all this mean for me. Nice tools that hide the engine from the user. isTAB for entering proteomics dfata. Its important to make things pretty. Login, security, tool remembers usage patterns. Previoulsy entered protocols, contac and factors, prevous searches using ontology lookup tool, remembers modifications to table structures and prediction of modifications in future. Basically nice for user - Cameron Neylon
Despite very effective tools for some things - but curation of submissions is still a huge issue. Array express will actually score MIAME compliance. Curation also a problem, assistance with pipelines. ProteoRED - hundres od miape compliatn reports collected via web forms. Elixr: contrusct a plan for the operation of a sustainable infrastructure for biodata in europe. Memorandum of understanding for implementation up to 500Meuro www.elixr-europe.org - Cameron Neylon
Standards for frunctional genomics: Divide by investigation - study - assay (experiment is far too loaded a term). Ontology of Biomedical Investigations http://obi.sourceforge.net Functional Genomics Experiment (FuGE) http://fuge .sourceforge.net - Cameron Neylon
Tracking evolution of MI-X can be a serious issue. Finding them can be a problem, checklists are all partially redundant. Arbitrary decisions make integration problematic. Signifiicant difficulties exist! -> MIBBI www.mibbi.org Central repository and foundy towards gradual integration. Find important things where metadata is required. MICheckout allows you to shop for concepts - generates Excel spread sheet (aaaaaargggggghhh!) or an XML schema. Paper out this month. - Cameron Neylon
Objectsion to MIAPE: WHy should _I_ dedicate reousrces to providing data to others (pro bono arguements that involve Genbank don't cut it) * This is just a 'make work scheme' for bioinformaticians (where is the credit for me) * I don't trust anyone elses data I'd rather repeat it (who the hell can afford this?!?) * How on earth am I supposed to do this (there aren't any mature free tools) - Cameron Neylon
Real benefits: Methods stay with data, no need to repeatedly construct sets of contextual information, avoids the risk of loss of information through staff turnover, 21 CFR Part 11 (the relevance of data can be assessed through summaries if you have good metadata), public data can be leveraged as commercial intelligence - Cameron Neylon
Argument over the imposition of ontologies on experimental science - answer that you can 'knock something up' using the formats but who is going to resource that? - Cameron Neylon
Going to start a new one as the previous one was getting long. - Cameron Neylon
Example of genome wide RNAi screens. Large scale datasets or large size. Could be seen as a pre-MIAME stage in comparison with DNA microarrays. Datasets can be hard to find, harder to analyse, serious hamburger issues. And nearly impossible to compare results from different labs - Cameron Neylon
RNAi globail initiative formed to bring researchers together. nearly thirty laboratories. Inforamtics Workgroup aims to develop tools to share and compare and analyse data. Challenges are to define which data to be shared, there is no current means to share it, therefore need standards and formats - Cameron Neylon
Important to distinguish between standards that specificy how to do an experiment and standards to describe how an experiment was done. Data standards are formal descirptions of the content of data sets. Metadata and raw data are both critical - not just processed data. - Cameron Neylon
Discussion of the importance of raw datasets. Suggestion that scientists want hamburgers not cows. Importance of re-checking the pdb with new refinement tools periodically mentioned so case for raw data robustly made. - Cameron Neylon
Data standards can also promote better practice in execution of experiments through SOPs and standardize the reporting of experiments. Processes need to be reasonably mature for this. Consistent use of procedures is required to make SOPs work. Segue into GLP and whether it applies to academic research - Cameron Neylon
Current practice is in the peer reviewed literature is insufficient to describe the experiment - Cameron Neylon
Did 1000 screens in ten labs with as close procedures as possible. Within group there is good technical reproducibility. Reproducibility between groups was poor. What is it we need to share to understand and define the differences? Built this based on standardisation exercise to accelerate development of standards. - Cameron Neylon
MIARE hosted at sourceforge. Issues of support for informatics in various groups. Development includes MIARE-TAB to enable excel based data input :) Need to harmonise standards -> MIBBI - Cameron Neylon
Will be trying to liveblog over the day here. Will see how it works out. - Cameron Neylon
BBSRC - can give steer from funder perspective but wanting to see community views and also educate where necessary. Interested in understanding sociological perspectives so bringing together the biologists and sociologists in this meeting. What are the key issues for BBSRC in data sharing? - Cameron Neylon
ESRC genomics network - research into sociology of data sharing in the biosciences. Issues of scale, organisation, technology. Social sciences trying to catch up with what is happening - Cameron Neylon
Been a request for me not to use names so I won't. Just report themes and comments. - Cameron Neylon
Research Information Network is starting up a project on Web2 tools in science - how are they useful? - Cameron Neylon
Mix of funders, scientists, sociologists and information managers - interesting group they've put together certainly - Cameron Neylon
Need both the willingness to share data and the tools to do so. NCRI working on systems for linking cancer resources together. Also interested in facilitating cultural change. Also talking to pharma about releasing data and trying to encourage that. Which company was it that made the recent announcement on pre-competitive data being made available? - Cameron Neylon
Is it possible to solve social issues with a technical solution? How to ensure acknowledgement for tool developers. Understanding the social issues associated with ontologies - move from OWL to SCOS(?) - do the possible technical solutions degrade quality? - Cameron Neylon
Idea of putting data sharing statements from grants in the public domain so people can check. How does BBSRC monitor compliance with data sharing. Issues of not very good data - should it be made public. Again we come back to the issue of sharing data that is not peer reviewed...and administrative load and predictability of that load, possible issues with IP that may arise in retrospect. The issue of 'hostile mining' of data e,g, animal experiments, stem cells etc. - Cameron Neylon
Answer back which is what I would have said - its important its out there and then you need a way to assess the quality. Peer review does not gauruntee data quality - Cameron Neylon
Science ethics course described given by scientists, lawyers, ethicists, economists etc - our (scientist's) perspective is just a perspective, and may not be a very good one. Other disciplines have very different (and possibly valid) perspectives. Potential ethical issues in pursuing sharing policies. - Cameron Neylon
Hit squad at NERC which aimed to provide every possible assistance to labs to get data into a database. Would go out, install computers, provide tools, support, be friendly (not sure about making coffee) etc etc. Sounds wonderful! - Cameron Neylon
Comment that the obsession with access control is less in companies (anyone in the company is perceived to have a 'right to see') than it is in academia. Some experiences that access control is more important to people than the tools. Scientists want control of where, how, and who can access their data. Prior disclosure is a serious issues for people coming to data sharing. - Cameron Neylon
Dataverse project- a loose database that can provide the data in reusable form close to the published papers. Interest from sociologists and cancer researchers (came out of WGS and gene expression data) - Cameron Neylon
JISC project to look at economic benefits of sharing data. Work has been done on costs but relatively little on economic benefits. - Cameron Neylon
Publications can't cope with presenting the data in their current form. If a data set is a terabyte, what goes in the paper? Current data transmission is insufficient. Funders not getting value for money. - Cameron Neylon
This was an introductory session with everyone introducing themselves - hence the collection of fairly scattering points - Cameron Neylon
BBSRC background - Data sharing policy: Policy has been in place for just over a year. Complements existing best practice guide for curation of data. 10 year period in a useable form is the BBSRC standard. *Biology is changing, large datasets, increasing use of datamining, increasing focus on QA and metadata. *Data sharing picked out early on as key area for Tools and Resources Strategy Panel, BBSRC should have leadership role in promoting appropriate research culture - Cameron Neylon
* BBSRC does not own data outputs (rights reside with institutions) but as a funder has interest in value for money. Is also a grant applicant (to government) *Development of data sharing policy to be inclusive and researcher led. Took three years over two stage consultation process - Cameron Neylon
From consultation exercise: Data sharing is a good thing! Critical (and well established) in some areas. Data sharing needs very different across different domains. IP and data sharing are tensioned. Should be no central silo. Decentralised sharing is preferred. Data should be close to the scientists (not sure what that actually means in practice - given how this flows into issues with Institutional repositories) - Cameron Neylon
Policy aim has two roles: Enforcement and aspirational signpost. Recognises the cost issues. Point out that data sharing is different to archival particularly with respect to costs. - Cameron Neylon
Other funders take different approaches - e.g. NERC has much more centralised approach. Potentially different issues in different domains. * BBSRC focusedd on big data and long time series but reserve the right to be more prescriptive in specific cases - Cameron Neylon
Where resources exist for sharing they should be used. If there is a need, create something, and ask for funding to do it! In some cases local ad hoc arrangements may be appropriate. * Will meet data sharing costs through FEC * Will provide resources to develop underpinning tools etc - Cameron Neylon
Issues of funding models - can ask for support in grant but will this work - serious problenmss in repositories charging for deposition. Wellcome trust model for OA where they deal with it and pay for it offline (independent from grant). Also a significant issues in training competent people to manage the curation process, where are these people? - Cameron Neylon
Proposals require a data sharing policy which is refereed by external reviewers against their knowledge of best practice. Expected to report at end of project.Now going into monitoring phase. Onus is on peer review of best practice. - Cameron Neylon
Overall good community buy in so far but big disparity in quality of responses. Some consternation. More mixed outside of established data sharing communities. Not much in the way of resource requests. Early days yet! * Challenges - can you measure value for money? Will it effect a sustained cultural change (or just grantsmanship?). Can understanding of best practice consistently applied by referees and panels? Are there barriers we don't know about yet? What unintended effects? - Cameron Neylon
Thanks, I've seen similar programs but they all stipulate that they are for visits to distant laboratories for training purposes, and tend to be in experimental biology areas. I'm looking for something more general that can fund trips to conferences or workshops, not exp bio related, not necessarily presenting a talk, etc... - Shirley Wu
I believe that many of the "institutional" conference organizers (CSHL, GRC, etc.) provide travel funds. I'm not sure about general funds for any conference (outside of the benefits that certain fellowships carry). Are you looking at anything in particular? - dsbreak
You mean like slush funds? It seems like it is rare for there to be a pot of money for unrestricted travel for students unless you get it through a general fellowship that gives a chunk of money that is unrestricted. I don't know if you can spend money from an NSF Dissertation Improvement Grant that way, but you have to get that funded for your research work. I think NSF Minority travel award might be another way, but only some qualify of course: http://rurl.org/u8o - Jason Stajich
Our graduate student association provides a few travel scholarships a year. - Mr. Gunn
Everyone Owns Science, trouble is, all these pesky publishers think they own science, slapping their restrictive copyright over everything :) - Duncan Hull
Nah - they just own the typesetting, the important stuff is in the public domain... - Cameron Neylon
I've tried to collate all the feedback that was given last time. Any more feedback on this version is welcome. I've outlined the focus of the survey in the first paragraph. - Michael Barton
I've just finished. Looks very good. Looking forwards to see the results. - Pawel Szczesny
'Liked' but I guess not filling it out - can hardly call myself a bioinformatician :) - Cameron Neylon
What Cam said. I "liked" it to give it extra juice here, make sure everyone sees it. - Bill Hooker
Michael was suggesting starting it officially on the 1st of July and let it run for a month before collecting the results and analyzing them. If we get enough numbers maybe the results will be interesting enough to send to a science news sections of some journal (The Scientists, Nature News, ...). If we get a bit of coordinated promotion on the 1st of July it would be great :D - Pedro Beltrao
I'm on holiday on 1 July - can I schedule a 'like' to pop in then? - Cameron Neylon
Send me a reminder, or post one here, and I'll blog the effort. Won't do much but every little bit helps. Betcha Jonathan Eisen would blog it too, and he has way more readers than me. Ditto Bora. - Bill Hooker
@Egon. I understand your point but I had to try and limit this question to a small subset of categories, so I used those from Bioinformatics. With too many, the analysis becomes less significant as it's spread out over a broader range. I know it's tenuous but metabolomics could be put under Systems Biology? - Michael Barton
After discussion with Pedro, we also thought it might be interesting to release all the data under a CC license so anyone can contribute to the analysis. Have to update the disclaimer at the top though. - Michael Barton
Well, in feel that bioinformatics is not just DNA/RNA sequence stuff, but the full biochemistry, but I recognize the thing that people say bioinformatics is blast++. A shame, really, because I thought the field recognized by now that an organism is more than it's blueprint. - Egon Willighagen
Done. I skipped the "bioinformatics tools apart from software development" - because I mostly write my own; and the "web applications" - because there's just way too many. Maybe a select list and then list up to 3 "other" would have been better. - Neil Saunders
I must admit that I was very underwhelmed by the article. Chris is a little out of his league isn't he? - Deepak via Bookmarklet
We were crunching the genome with huge clusters a decade ago. As we get more information, our models get better. To make more sense of this information our theory has to get better to as Lee Hood always says. Ah ... I am bugged. All Hypy with limited fundamental understanding - Deepak
I'd like to see someone try to sell 'correlation is enough' to the FDA or equivalent - Cameron Neylon
Cameron: lol In journalistic terms the essay is good, but it's science where being only trend sensitive is not enough. And Anderson has not much clue on what's going on in biology, but he is probably right on what's going on in physics, which we don't really know. - Attila Csordas
Am reading the paper version of Wired at this very moment! The cover uses the headline "The End of Science." Now that caught my attention as I pulled it out of the mailbox! But yes, underwhelming. I don't think scientists are going to stop asking "why?" anytime soon, the way the article makes it sound. - Shirley Wu
like I said last time this came through - it's a tad grandiose. Did he just learn about data mining recently? - Mr. Gunn
Ah - plane travel tomorrow which is usually when I buy a copy- mind you probably be last months on this side of the pond anyway :) - Cameron Neylon
I agree, Bill. Makes one think of the many propositions to replace wet lab experiments with in silico substitutions. You need both. - Heather
Chris still is onto something. In industry you can create value from correlations and "hunches" based on data. Even medical trials are just data and correlations. And in oder to save lives you don't really need to know why, just what. Science is a method, never forget that. Not a religion. And its limits are there, as well as its advantages. Other methods might be more efficient at doing something else, not? - dekay
Actually, that used to be the case. The focus these days is on the why, on the mechanisms. It's why VIOXX happens, cause you don't understand the why. Yes, you need statistical separation, you always have, even when you had limited data. More data only improves your statistics. - Deepak
For example, docking studies are increasingly trying to add more "physical" measures rather than rule based implicit, this is what the data tells us measures. Science is much too noisy, and the kinds of false positives you would get with Google are NOT acceptable. Is the scientific methods dogma. Can it change, yes, but not for the reasons that Chris is talking about - Deepak
Even Valleywag has an opinion on this, they are scientists too, and have a lab at the back: http://valleywag.com/5019748/w... "The problem here is that if we stop asking the question "why?" then we are basically making for the foundations of faith. You can always make statistics say nearly anything you want, it simply depends on the assumptions you make when you analyze and present them" - Attila Csordas
Attila - no, Anderson is definitely not right about physics, either. It's a strange article. Data mining isn't replacing the old scientific method. It's augmenting it. - Michael Nielsen
Agree with Michael. The writer seems to think that somewhere in a big pile of data lies "everything", waiting to be extracted using algorithms. That's just not how science works. It's the questions that we ask and the interpretations that we devise that make it science, not the raw information. - Neil Saunders
I created a slide at my previous job, which had all the data sources (expression, proteomics, genotyping, histopath, name it) that exist related to a study on the edges, with the emphasis on there being a ton of heterogenous data, and in the middle a big "?". The point. It's all about the question, NOT the technology or data type - Deepak
Chris' piece is provacative ... but the Ars Tecnica piece touches on some key points - was /.-ed a bit ago, so my apologies if this is old news: http://arstechnica.com/news.ar... - Kaitlin Thaney
Kaitlin, that is a great article. Hopefully it will help the masses understand why Anderson is wrong. It also leads to a worry I have had about Google. They don't really understand science at a fundamental level. Maybe I am wrong, but I get that impression all too often. - Deepak
Although I admit I don't quite get the cloud part. It almost seems incidental - Deepak
Hey Deepak. Don't tell Attila you don't think Google gets science. ;-) - Mr. Gunn
There's a good "rebuttal" on ArsTechnica (see comments to Wired piece for a link). Also discussion on Nature Network Cancerevo blog (on the computing clouds) and at the Researchers and Web 2.0 group which you are all warmly welcome to join (I sent round an invite just now with the link). - Maxine
what's on? wrong side of town for me anyway and need to be on road to bristol airport at 4:30am tomorrow but always worth knowing what's on - Cameron Neylon
I'd like to note that no bioinformaticians appear in this list, despite our profession's numerous risks. - Chris Lasher
To be fair, most of these guys pre-date bioinformatics...or indeed informatics. But I would be worried about the cluster falling on you...yes, that one....ITS BEHIND YOU!!! - Cameron Neylon
Hmm. Good idea, as I posted on the blog directly. When I get my feet here I will make fewer mistakes. - Heather
You'll be all conferenced out before you know it. Hope to see you again at BarCamb and/or PSB - Duncan Hull
Wow that's quite the lineup - makes a good list of open science events too. - Richard Akerman
Yep - its a bit scarey in aggregate. Wondering whether I can do the North Carolina meeting on the way back from Hawaii... - Cameron Neylon
Well Euan posted there (on the blog) that we should all use Dopplr but I'm not sure that I can take another webservice on at the moment :) Duncan, will you make it down to London and/or Soton in late August? Heather, they're not mistakes, they're explorations of the medium... - Cameron Neylon
