Andrew Su - Comments

Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing http://bib.oxfordjournals.org/cgi...

Friday - Comment - Like - Share

Please email http://is.gd/Ag43 Thanks! - Iddo Friedberg

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access denied - Graham Steel

sent.. - Andrew Su

gone - Kubke

Thanks Andrew & Kubke! - Iddo Friedberg

John Hogenesch

A brand new faculty member (elsewhere) asked me when they should put in their first R01. Given January 25, recycled challenge grants, new format, etc, any thoughts?

Friday from iPhone - Comment - Like - Share

if it were me, I'd do it as soon as I felt like I had a decent proposal ready. With only three cycles per year, you only get so many shots on goal, and all feedback/experience is good... IMHO... - Andrew Su

I think it's likely that a new R01 could get lost in the shuffle in January -- as you said, you only have 2 shots on goal. It may take a few cycles to flush the "challenged" grants out of the system. - John Hogenesch

Michael Kuhn

congrats to @larsjuhljensen et al: the current issue of Cell contains Reflect tags! http://beta.cell.com/index...

Friday from Twitter - Comment - Like - Share

Duncan Hull, Rafael Sidi, Andrew Su and 4 other people liked this

How can I not like this :-D - Lars Juhl Jensen

In addition to "Literature, Sequence, Structure...", how about "Expression" with a link to BioGPS? just a thought... ;) - Andrew Su

Mr. Gunn to Mr.'s feed, The Life Scientists

I need some feedback/career advice.

November 8 - Comment - Like - Share

Bora Zivkovic, TheIndustryStandard, Meryn Stol and 23 other people liked this

Many of you know I've been working with Mendeley as a sort of ambassador/community liaison. I started this because I've always felt a little shut out from contributing to open science/open access/open data because I don't work for a publisher, don't really write code, and wasn't in a job where I could openly share data. This was a way to influence how things develop by promoting the people who "get it". - Mr. Gunn

41 more comments

I had to quit for the "real job" a little while back and found not only that I had more time to work for Mendeley, but that I started getting other offers/opportunities also. - Mr. Gunn

Now I've got a newborn daughter and am liking the time I can spend at home with her, which raises the following conundrum: Can I do more of this community liaison work for companies that support/promote open access and put my research career on hold, or is there not any future in this? - Mr. Gunn

Can I trust the friends and colleagues I've met on here to be able to have a real discussion with me, keep me honest, and tell me if I'm backing the wrong horse as I take on more clients, or would I be considered a sell-out? Would people believe that my opinions still come from me and my experiences, or would people just think "You're only saying/supporting that because they're paying... more... - Mr. Gunn

Do you think there's room to grow in this kind of role or am I just wishfully thinking that I can make my own job in this tough economy and get to spend time with my daughter too? - Mr. Gunn

I really believe this is a way I can contribute to changing how science is being done, opening up the process, disintermediating scientific discovery, and all those noble sounding things, but do you buy it, or do you think I'll not only become corrupted by money but lose my relevance because I'm not really doing science anymore? - Mr. Gunn

Can I help companies that don't quite get it to improve and become better and more responsive to their community of users or will I lose touch? - Mr. Gunn

I will be saying nothing works better than inspiring people by setting examples, I will not go with holding my research career even it is not working well as long as I have passion for discovering something. But there are certain realities and money is one of them. Ambassador/community liaisoning is other way to contribute back to the science, but it will be too early to give up your... more... - Abhishek Tiwari

Mr. Gunn. You can absolutely do so, but as you note, you cannot do this with one client. It will have to be a consulting/pundit role (you should probably have a chat with Paul Miller at some point http://cloudofdata.com). The life science industry will be challenging given the limited opportunities, and in this economy, this will not be a walk in the park. As to whether you have to be... more... - Deepak Singh

And we'll tell you if you're being an idiot. It also depends on what you really want to earn. You're not going to get rich doing this, at least not quickly. - Deepak Singh

Abhishek, I could cite all the times when I've recommended Papers or Zotero instead because it really was better for what the person was looking for as evidence that I don't always have to say what the official line is, but that wouldn't illustrate all the discussions I've had where the company point of view _became_ my point of view. This is exactly the kind of discussion I want to be... more... - Mr. Gunn

Thanks Deepak. I know you will, and I'm not looking to get rich. I'm looking to do work for people I believe it, be a force for good, and at least for the moment, spend more time at home with my daughter. - Mr. Gunn

Mr. Gunn, it will only taint it if you let it, although there will people who'll always be skeptical. As long as you are honest and present your point of view rationally, you'll be fine - Deepak Singh

I'd like to think that being open and transparent online helps illustrate my biases, too. - Mr. Gunn

Way outside my area of expertise, but I would think the "consulting/pundit" thing that Deepak mentions would involve lots of travel, especially to start. Not sure how conducive that is to spending more time at home... - Andrew Su

Andrew, missed that bit. There would be a fair bit of travel - Deepak Singh from iPhone

Tough call MrG. I'm not concerned about you selling out, plus I will call you out if I think you are sliding into that trap (as, I'm sure, will the rest of the FF posse). My larger concern would be whether you can make a living that way. Is there a more regular (but part-time) gig that you could get to buffer the difficulties of forging a new path? For instance, do you write easily and... more... - Bill Hooker

Having a part-time gig would allow you more freedom to take risks and experiment, and could be phased out as and when your liaison/consulting work grew. - Bill Hooker

Bill, that's a really great idea. My current commitments are only part-time, so having something more steady would both help the bottom line and insulate me from selling-out criticism - "I don't need to do this." Please, put me in touch. - Mr. Gunn

the ultimate evidence for or against bias is behavior, would such a position restrict or inhibit assuming a critical perspective? - Mike Chelen

What fun would that be, Mike? I just wanted to do a sanity check against my friends and colleagues here to make sure that at least some of them would promise to call me out if I started to not make any sense or drift away from the principles of openness this community takes as a fundamental principle. - Mr. Gunn

Interesting situation! My take is that people who have no history of interaction with you, will not spend a lot of time looking you up online. As soon as they know you're being paid to do this, you'll be a sales rep - which means there isn't even any need to look you up, they already know who/what you are. Thus, IMHO, no online history will get you out of the sales rep box. - Björn Brembs

I agree with Bill's suggestion, and also his non-worry about bias. Or rather, we're all biased, but you don't come across as a sell-out company mouthpiece to those who know you, so you can let that slide. Bjorn isn't tender, but he's right. Either way, you won't change it by adding on more opportunities to be a facilitator. And forging your own path to be more with your family - having been there, I would say you won't regret it later. One always has career regrets, but that's because we only have one life. - Heather

Mr. Gunn. A full time liaison for a company will effectively make you sort of a sales rep. I have been a sales rep myself - which was a valuable learning experience, but I suspect, like me, not one you would fit comfortable into for a longer period of time (several years). When I left university, my friends and colleagues told me that I had a time-limit of 1-2 years to get back into... more... - Nils Reinton

Thanks, Nils, Heather, Björn. My intent is not to work full-time for a specific company, and I'm not doing that now. My intent is also to talk more about ideas and trends and less about specific products. Although I do spend a fair amount of time recommending Mendeley, I think Zotero shares their mission and I just personally prefer Mendeley. I used Zotero to write my first paper and it came down to me just wanting a desktop, full-screen app instead of their browser add on. - Mr. Gunn

Björn - We all have our various reasons to believe what we do and say what we do. In my role, I'm not being paid to say anything or to have a certain opinion. In fact, I think where I disagree with the Mendeley guys is more valuable to them than where I agree, because what they're basically paying me for is my insights as a scientist who knows the field and keeps current with... more... - Mr. Gunn

I know I can't speak for anyone, and I'm not appointing myself spokesperson, but if I spend a lot of time listening to, talking about, and synthesizing ideas, and I can also effectively market those ideas to people who need to hear them (that is, companies who want to listen and adapt), isn't that a win? Couldn't that be my way to make a positive contribution to open access and linked data and personalized medicine and these causes that I already believe passionately in? - Mr. Gunn

"Couldn't that be my way to make a positive contribution to open access and linked data and personalized medicine and these causes that I already believe passionately in?" YES, absolutely, you are already doing this very well. If you can make a living out of it, I salute you :-) - Nils Reinton

Perhaps consider not just consultancy for companies, but also undertake work for public sector agencies (major libraries or funders), charities or not-for-profit companies. - Frank Norman

Mr. Gunn - sure I think such a person would definitely be worthwhile to us! I was referring to people who do not know you: if you approach them and tell them you work for company X, my bet is that most of them will think "ah, he's a failed scientist trying to get me to use their products". Of course, this doesn't stop people from using company X's products (or sales reps would die out... more... - Björn Brembs

this is a great thread, Mr. Gunn, cheers for starting it, very interesting points, everyone; I would like to second Nils and Frank, and I think that some journals might also be interested in your advice (and community liaison work) and that this would certainly be a great service for anyone near to being an OA and linked data addict - isn't this a pretty wide range of users? we might create a list of arguments that you might wish to choose from when talking to journal publishers - test them on me ;-) - Claudia Koltzenburg

Mr Gunn...you might know me from the ChemSpider system. For almost 3 years ChemSpider was run as a "for the community" project at my cost. i.e. My wife and kids lost a lot of access to me, despite the fact that I worked from home. It did NOT pay any bills...it just about covered costs. No, I was a consultant for a number of companies and worked hard for them, traveled a lot and used my... more... - Antony Williams

OT b/c it's blog not job related *but* I would cite this FF thread at some stage in this one. http://ff.im/YB4p from Feb '09. - Graham Steel

Nils, thanks! Frank - that's a great idea. Can anyone put me in touch with someone at one of those agencies/companies? Björn - I see what you mean. Online rep doesn't translate offline automatically. Claudia - I've got a series of arguments, gleaned over the years from participation here and elsewhere. Can I send you an email? Antony - yes, I'm familiar with your work, and I have a... more... - Mr. Gunn

Mr. Gunn, one thing I've noticed in recent conversation with doctors (not academic MDs) is that most do not know much at all about OA, aren't sure what to make of a statistics-rich, data-driven science environment (or how to connect that data to actual human patients), and are leery about packages being hawked to them. Many are similar to me in age, meaning they didn't grow up in a... more... - Mickey Schafer

Well, I see myself being able to help in explaining these issues, but I don't think I'd get too far hawking products. I'm just not that kind of person. - Mr. Gunn

Even products you truly believed were worthwhile? - Jack (a.k.a. Jeber)

Yeah, I just don't think I'm the salesman type. I think I'm more effective developing ideas than products. - Mr. Gunn

You don't have to be a salesman to develop products. Product development requires a better understanding of customer needs than anything else out there. Being a product manager was one of the most satisfying jobs of my life - Deepak Singh from IM

Mr. Gunn -- I wasn't suggesting that you represent product -- actually, I was thinking more in terms of a "knowledge broker" -- the slow adoption of some technologies (whatever they may be) is often b/c the persons needing the tools don't know how to evaluate them -- sometimes, they may not know how to evaluate their own needs. Having an expert who can help someone understand the landscape, help them make choices based on needs (as opposed to sales pitches) is a very valuable resource. Just a thought! - Mickey Schafer

Another area that is worth looking at, though probably represents a short term play, is that there are lots of people out there putting out calls for tenders to do small research projects in the Social Media/Publishing/Data/Science space. Again its patchy, and not regular but with some reliable money coming in from e.g. editing and writing this kind of work could do two things, firstly... more... - Cameron Neylon

MrG, did you get my email? I sent it to a gmail address that I have listed for you in my address book. - Bill Hooker

Yes, I got the one you sent and I really appreciate it. I do plan to follow up when I get back into town. - Mr. Gunn

Neil Saunders

To be honest, choice of non-MySQL DBs is rather bewildering: HBase, Hypertable, Cassandra, non-relational (Mongo, Tokyo, Couch)...

Wednesday from Twitter - Comment - Like - Share

We've only played around with Couch, but I've got to say I've been pretty blown away by it, both in terms of ease of use and power. All else being equal, I'd say that would be a good place to start playing... - Andrew Su

Egon Willighagen

Frequency of a Term via PubMed - http://blog.rguha.net/?p=443

November 11 from Google Reader - Comment - Like - Share

Rafael Sidi, Benjamin Tseng, Frank and 8 other people liked this

Liking this very much! Thanx, Rajarshi! - Egon Willighagen

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E.g the rise of "ontology" http://rest.rguha.net/usage... and semantic http://rest.rguha.net/usage... have we reached the peak yet? - Duncan Hull

@Rajarshi a small bug: nothing was displayed with http://rest.rguha.net/usage... whereas the NCBI returns about ~9000 articles http://eutils.ncbi.nlm.nih.gov/entrez... - Pierre Lindenbaum

the site is a little slow, but a while ago I saw this tool for looking at PubMed trends on the internets: http://www.cotch.net/assed... - Michael Kuhn

@Pierre, thanks for the catch. I actually do get the correct data. The absence of bars seems to be a limitation of the Google Charts API and the max size of the chart image. If the X-axis is too long, the bars need to be thinner for it to fit into the plot area, and you can only go so thin and then loose readbility. Like I said - this is a quick hack :) Ideally I'd use matplotlib or R as the backend for plotting, but am lazy right now - Rajarshi Guha

interesting, and very cool. One question/comment, does the Google Charts API by default adjust the image so that the x-axis crosses at a non-zero point on the y-axis? I'm sure that breaks one of Tufte's rules about misleading graphs... - Andrew Su

@Andrew - yes. It took me a bit for me to realize that the count for the first year was not always zero! The Charts API does have a way to set the y range, but I'm going via the pygooglechart Python module which doesn't seem to support that. - Rajarshi Guha

i was about the link to my pubmed trends tool, but i see it has already been done :) it is indeed slow -- a clunky php proof of concept really. (it has been especially slow today because apache filled itself with processes that were trying to do i'm not sure what...) http://www.cotch.net/assed... - Joe Dunckley

Andrew Su

New home page - http://biogps.blogspot.com/2009...

November 5 from BioGPS - Comment - Like - Share

Ami Iida, Pierre Lindenbaum and Chris Lasher liked this

How nice to have a scientific site that doesn't look like it came from 1996. I will note that on Ubuntu 9.04 in Firefox 3.0, I get sluggish scrolling on the home page, but I'll be up to 3.5 soon and I think that should help. Anyway, looks lovely and feels otherwise very usable. Great work. - Chris Lasher

Thanks Chris. Will make a special note to do some testing to see if we can fix that sluggish scrolling... - Andrew Su

Useful that. - John Hogenesch

The Life Scientists: Steve Koch

What's the best way to embed a pdb crystal structure into a wikipedia article? Is there a gadget that allows reader to rotate & zoom? Or is static png the way to go?

November 1 - Comment - Like - Share

Jane Breezler, Paul Bacchus, Konrad Förstner and 4 other people liked this

How about an animated gif rotating it? - Ruchira S. Datta

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I agree that's better. I didn't know how to do it easily, so just put a snapshot in. It's my new stub article on Tus: http://en.wikipedia.org/wiki... - Steve Koch

I realized what I actually want: A widget that will display a molecular dynamics trajectory of the system, while allowing user to rotate, zoom, pull on atoms, etc. ... Comp. people get to work :) - Steve Koch

One of the web widgets they offer at the PDB might work in the context of Wikipedia but I would guess this is one to have a wider conversation about? Andrew Su and Tony Williams would have an idea of the logistics at least. - Cameron Neylon

The Jmol community has been trying for a long time now to get it available in Wikipedia... you could ask on jmol-users@ ... - Egon Willighagen

For small molecules, Noel's TwirlyMol looks nice http://baoilleach.blogspot.com/2009... , as it doesn't require plugins. But it doesn't seem to scale well for proteins. - Pawel Szczesny

Steve, try asking on http://sciencestack.com. - Jane Breezler

There's a long and tangentially relevant discussion here http://en.wikipedia.org/wiki.... As Egon alludes to, there is an effort to get the Jmol extension installed, but I don't see much activity http://en.wikipedia.org/wiki.... Proteopedia has Jmol: http://www.proteopedia.org. - Andrew Su

As part of the Gene Wiki effort, we uploaded ~66k thumbnail images created by the EBI to wikicommons, and categorized them by SCOP. http://commons.wikimedia.org/wiki... Of course, they are auto-generated so they probably don't illustrate what you'd want to illustrate.. (and certainly not an MD trajectory...) - Andrew Su

Thanks! Oh, and BTW, I was kidding about the MD trajectory, including the ability for the reader to pull on atoms in a real-time MD simulation. :) - Steve Koch

Jmol has been up for discussion for a long time. I am not aware of any movement to support it at present. You might want to put the crystal structure hosted in Jmol elsewhere and make a link to it from the Wikipedia page rather than having it in the Wikipedia article itself. - Antony Williams

The Life Scientists: Rajarshi Guha

Question for bioinformatics experts: given a gene name is there a good way to identify papers talking about it? An obvious approach is to do a Pubmed search and see how many hits. But seems a little rough. Is there anything better ?

November 4 - Comment - Like - Share

Piotr Byzia, novoseek, Khader Shameer and 6 other people liked this

ncbi maintains both gene2pubmed and geneRIFs, but neither should be considered comprehensive... - Andrew Su

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You can query ncbi:eutils/elink e.g. http://eutils.ncbi.nlm.nih.gov/entrez... but, as said, Andrew, the database is not fully complete. - Pierre Lindenbaum

www.novoseek.com/, www.nextbio.com, biosemantics.org/geneE/search.jsf, and www.ihop-net.org are some resources... - Jeff Kiefer

Thanks for the pointers, useful to start with - Rajarshi Guha

The trick is not to start with a PubMed search for the gene name, but to start with the NCBI Gene database. All of the Entrez databases are linked so you can go from a Gene record to publications. Use either EUtils as Pierre and Andrew said, or go from the Gene page (e.g. http://www.ncbi.nlm.nih.gov/gene...) and follow the links. - Neil Saunders

geneRIFs might not be complete, but how complete do you need to be? - Mr. Gunn

@Mr Gunn, my application doesn't really need authoritative information. Basically, I'm trying to get a rough idea of which genes are more popular than others in terms of publications. Given that a pub may mention a number of genes in passing, it's not a very reliable measure. But it's one other feature that I can use in a summary/ranking etc - Rajarshi Guha

Rajarshi, it sounds similar to an analysis that we did previously to create what John Hogenesch calls the "sexy gene list". See http://www.ncbi.nlm.nih.gov/pubmed... and Figure 1 of http://www.ncbi.nlm.nih.gov/pubmed.... We used gene2pubmed (ftp://ftp.ncbi.nih.gov/gene/DATA/) and an awk/sort/uniq one-liner ... - Andrew Su

@Andrew, thanks for those papers. Yes, my "novelty score" is pretty much what you did - Rajarshi Guha

Deepak Singh

Yet another middle seat. My flying karma is bad these days

October 27 from Twitter - Comment - Like - Share

Did you forget to smile charmingly at the ticket agent? - Chris Lasher

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Those blasted machines are immune to my charms - Deepak Singh from iPhone

how is it possible that you don't have enough miles to get upgrades to the soft and plushy seats every time? - Andrew Su

My miles are scattered between 3 airlines - Deepak Singh from iPhone

I feel your pain, Deepak -- status for me is like the pot of gold at the end of the rainbow -- its always *just* out of reach no matter how hard I try/take business trips - Benjamin Tseng

Domestic travel is just hard. Last time I had gold status I was traveling internationally all the time - Deepak Singh

Björn Brembs

Lessons from SfN 2009: scientific societies are not social - http://bjoern.brembs.net/news...

October 23 from bjoern.brembs.blog : a... - Comment - Like - Share

Gediminas Luksys, Kubke, Noah Gray and 6 other people liked this

"Why does a scientific society have to go to Facebook for social web technology? Why doesn't it have that technology built-in? After all, social and society don't share the same etymological ancestry for nothing (i.e., the Latin word socius meaning "companion"). I'm sure over 40,000 members are a large enough base where most current tools would work fine. For instance, imagine you could have a buddy-list of other SfN members. Then, when the program of the next meeting is available, you can choose to pre-populate your itinerary automatically with all the presentations by your buddies." - Björn Brembs

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I think the problem might be hassle of getting permission to automatically add members - and when asked probably the vast majority will ignore the request. Then even if there is a network I suspect it will be accessible only to members of that society. - Jean-Claude Bradley

The idea is to be only accessible to members - after all they're already using the site for plenty of other things anyway. The idea is that societies should use social web technology to deliver the kind of improvements societies were founded for initially: improved communication between members with a common interest. - Björn Brembs

maybe I'm in the minority here but for me one of the biggest advantages of social software is meeting people you didn't know existed - so I don't see the incentive in participating in a closed network - Jean-Claude Bradley

But there's a cross-incentive for the society to CREATE a closed network: lock-in, perceived "added value" for the membership dollar. In my experience such closed networks don't fly, for exactly the reason Jean-Claude adduces, but that doesn't stop orgs from trying. Also, I've run into real snobs, who don't want to engage in what they perceive as a free-for-all but are more interested in a walled garden. - D0r0th34

Good points! Indeed, because in principal every member of these societies could meet in meatspace, meeting new people is *not* one of the goals I had in mind. Rather, keeping track of who of the 40,000 members of SfN is doing what. I regularly miss people or their presentations at meetings, simply because I don't have the full record of people in my head at all times. If there were a way of tracking their activities automatically, this would be easier. - Björn Brembs

Basically, my idea was to leverage social web technology to have people spend *less* time on the society's website, but getting *more* done. This may only work for large societies, where the number of people in your field attending has become too large to track by hand, but science in growing... - Björn Brembs

Scientific societies are anti-social in general - Alexey from iPhone

how about having a SFN society / group on NING. Only sfn members may be added to the social network and it may be what you desire...though being a non-member (and having no hope of becoming a member) I'll always support open forums:-) - Sandeep Gautam

Sounds to me like something to aggregate information held elsewhere, rather than something you'd build, Bjorn. Take from Facebook, TripIt, Dopplr, and maybe you'd have something. - D0r0th34

I don't think I've made myself clear at all. Maybe an example will help: Every year, I try to remember every name of every person I know who may possibly attend the SfN meeting. I spend several hours populating my online itinerary (with their presentations as well as by keyword), only to always forget some individuals. Now, if I had a buddy list on the SfN website (where I go regularly... more... - Björn Brembs

OK - that makes sense Bjorn - Jean-Claude Bradley

That's a great idea Bjorn. Especially at a meeting like that which is so enormous! It'd be nice (and really easy to program) an automatic itinerary generator. - Brian Krueger - LabSpaces

IMHO, what defines a "social network" is not who's in the network, but what you want to do with the network. I think what you're describing are still social activities (tracking other people's movements and activities) and I think they're not unique to scientists. Therefore, I think SfN is right to go after a generic network like FB. This is the part that I think the "FB for scientists"... more... - Andrew Su

As part of the selected few to try out the RSC's new 'social networking' site (which doesn't have the same good ideas to be fair that Bjorn has suggested (at least not yet)), my (and my peers) view is that it is just _another_ site that needs to be logged into, checked, etc. The reason we all suggested FB was that 1. all of us were already using it and 2. we had already initiated... more... - Anna Croft

Anna and Andrew, those are great points and make a lot of sense! I know too well how little I want to have to track yet another site. In this case, one would have to find a way to get the functionality implemented on FB, I wouldn't mind that at all - as long as I have the functionality. It would also still have the added benefit of scientists using FB for science. - Björn Brembs

On the other hand, every single attendee of SfN (30,000 every year) *has* to use the SfN website just to see the program (or get accommodation!) and without your own itinerary, you're basically totally screwed. In other words, disregarding the website is not an option, tens of thousands of people are using it already anyway, most of them also more than just once a year. The society's... more... - Björn Brembs

Bjorn, I think you're right, if SfN (or ISMB) made a FB app to track the program, speakers, and attendees, I think that would be pretty fricken cool. And, I think, more productive than trying to reimplement a social networking site from scratch. - Andrew Su

Paul Gardner

Breakfast: Dead Bunny Toss - http://www.youtube.com/watch...

October 24 from Facebook - Comment - Like - Share

"Throwing dead bunnies is WRONG WRONG WRONG. You are likely to get greater distance throwing live bunnies..." Hilarious! (not that I condone either...) - Andrew Su

Classic kiwi humour. I can't wait to go back and try some [dead] rabbit throwing. Could try possums too. Both are major pest species there. - Paul Gardner

References Wanted: Chris Lasher

"Comparative transcriptional analysis of embryoid body versus two-dimensional differentiation of murine embryonic stem cells." Sepulveda et al. http://www.liebertonline.com/doi...

October 22 - Comment - Like - Share

chris dot lasher [at] gmail dot com, TIA! - Chris Lasher

3 more comments

I get an error at the publisher site: "The requested article is not currently available on this site." - Andrew Su

Ah, my apologies! That PubMed link wasn't resolving correctly to the publisher. I provided a direct link to the publisher in the entry, now. (Sorry!) - Chris Lasher

Sent. - Bill Hooker

Thanks!!! - Chris Lasher

Andrew Su

Thinking of going to dreamhost to host a new drupal version of http://sdcsb.org (replacing hand-coded HTML hosted by UCSD). Good idea? Comments on any part of this plan welcome...

October 20 - Comment - Like - Share

Deos it have to be drupal? If there is a Django CMS you could host it for free on Google App Engine. Or Heroku for a Ruby CMS. - delagoya

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I initially thought drupal because it's relatively mature. But I like the ideas above. Anyone know of actual deployments of a CMS on GAE/Heroku? - Andrew Su

Rich Apodaca has Chempedia working on Heroku. I suspect that's a custom Rails CMS, but any Rails app should work. Workhabit have a Drupal AMI for EC2 http://www.workhabit.com/labs... - Deepak Singh

For Ruby, there is RadiantCMS, and a newer CMS called Seed that looks promising: http://www.railsinside.com/tools.... Another option would be hosted wordpress.com with custom theme and hostname, although I do not know UCSD's policy on CNAME records that should point to their internal network (although sdcsb.org looks like something they should have no problem with). - delagoya

Don't know about Dreamhost. Choosing a host is always a bit of a minefield. Personally, I use A2 hosting which has been very good. I have built a websites in both Drupal and Wordpress in the past and I would say that if the functionality exists in Wordpress then I would go with that every time. Drupal customization is a nightmare in comparison. It's very flexible, but unless you enjoy... more... - Matt Leifer

Great feedback, thanks guys. Will definitely go check out wordpress for the simplicity factor. Entering the aforementioned minefield, any other hosting recommendations? Seems everyone offers unlimited bandwidth/storage now, the differentiating factors seem pretty slim... - Andrew Su

No, the differentiating factors are *very* large, it is just that you can't tell what they are from the blurb on the hosts own site. For instance, I started out with Servage before switching to A2 because Servage is incredibly bad, but you wouldn't be able to tell the difference by looking at their sites. Unfortunately, it is also very hard to find an unbiased review site that is not... more... - Matt Leifer

At the risk of repeating myself, if wordpress is leading the pack, you should seriously think about hosting it on wordpress.com. For $40 (no ads + domain map) they maintain the servers, apply updates and security patches, etc. The only reason to host it yourself is of course if you need a custom theme, and frankly I host with go-daddy (which is the used-car salesman of hosting) and have never had a problem with their cheapest economy plan. Plus use coupon code WORDPRESS2 for a discount! - delagoya

D, my impression was that wordpress.com was too limited for what we'd want to do (single-blog focus), but it will definitely be something I check out to confirm. Matt, fantastic set of criteria for evaluating hosting companies. Thanks again to you both... - Andrew Su

The Life Scientists: Walter Jessen

There must be a better way to do search for matching values between tables than using VLOOKUP in Excel (i.e. search for a value in the first column of a table array and return a value in the same row from another column). In Snow Leopard, Excel 2008 chokes on 40k rows. Is there a shell script? Perl? I'm open to suggestions. How are you searching?

October 20 - Comment - Like - Share

Mike Chelen liked this

unix join command, or perl hashes are much more flexible (but a little more work) - Andrew Su

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awk - excel for the commandline - Anders Norgaard

unix join, mysql, sqllite ... - Pierre Lindenbaum

Galaxy http://main.g2.bx.psu.edu/ "Join, Subtract and Group" - Pierre Lindenbaum

open office spreadsheet has a match() function http://wiki.services.openoffice.org/wiki... that has worked alright with many rows. otherwise awk sounds good, or throw it into a database like mysql - Mike Chelen

Bill Hooker to Bill's feed, Science 2.0

2020: A Publishing Odyssey - a knol by Ahmed Hindawi - http://knol.google.com/k...

October 20 from Bookmarklet - Comment - Like - Share

Duncan Hull liked this

"The possible futures of scholarly journal publishing This article is based on a talk given by the author at the 32nd UKSG Annual Conference, Torquay, UK, March 30–April 1, 2009 and first appeared in Serials, Volume 22, Number 2, Pages 99-103, 2009, doi:10.1629/2299. The information industry landscape is changing at a rate that would have been unimaginable just a few years ago. As the digital revolution continues to unfold, many existing publishing enterprises will either cease to exist or be transformed into a form that is virtually unrecognizable from their current one. Three factors will shape the future of scholarly journal publishing: the success of open access versus toll access business models, the survival of the journal brand on the author side, and the survival of the journal brand on the reader/librarian side. Whether you find some of these possible futures desirable or catastrophic depends on who you are." - Bill Hooker from Bookmarklet

There are people writing knols? - Andrew Su

delagoya

Slides for CouchDB talk are done! A whole day ahead of time! This is a new record for me #fb

October 20 from Twitter - Comment - Like - Share

willing to share them later I hope? - Andrew Su

Andrew Su

bioperl has a mantra that I paraphrase as "working code wins" -- meaning practical implementation trumps theoretical arguments for the "right" way of doing something. Anyone know where this is described?

October 15 - Comment - Like - Share

Khader Shameer, Abhishek Tiwari, Frank and 3 other people liked this

Chapter 1 of Coders at Work. Although with my years with Perl code I am not so sure :) - Deepak Singh from iPhone

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Ahh, dates back at least to BOSC 2002 from a talk by Jason Stajich http://open-bio.org/bosc200.... I couldn't find it on bioperl.org which is why I thought I was remembering it wrong. But perhaps this has been retired as "official" Bioperl dogma? - Andrew Su

Ah there was formal dogma? I was almost done with Perl by 2002 :) - Deepak Singh

You know, I too was pretty much done learning perl in 2002, but the crazy thing is that my 2002-perl knowledge still allows me to do 90% of what I want to do. Anyway, hopefully Jason will chime in here with the official line... - Andrew Su

It hasn't changed much since 2002. I am pretty sure Jason has the official line. I just liked the basic Perl motto: TIMTOWDI. - Deepak Singh

worse is better - Bosco Ho

Uh Oh. This is going to get ugly - Deepak Singh

Once every ~6 months I convince myself that I should drop perl but every time there is something that needs to be done for yesterday and puff there goes the motivation. Its so hard to change when the transition is a period of veryyyyy annoying inefficiency - Pedro Beltrao

Pretty sure Ewan Birney popularized this; I remember it along the lines of "the first one to code it wins." The idea being that you can discuss object models and the right way to do things all day, but in the end working, easy to use code is what people are going to adopt. I don't remember if there is an official description of the thought process; probably too busy coding. - Brad Chapman

Unfortunately, this hides the idea that code is more than the an algorithm. If you had some clearly written, well documented, simple and well designed code which a new version of blast had broken, and a pile of spaghetti which happened to have been written more recently, perhaps it would make sense to dump the latter and fix the former. You can go too far with perfect design, of course, but you can go too far with macho programming as well. - Phil Lord

I think Ewan was the originator - I think I was just restating the motto. There was some design/developer philosophy in the bioperl.pod that also probably included this. The philosophy is that lots of mailing lists (where our dev is primarily coordinated) are filled with people spouting or complaining about things not being perfect, but in the end working code would win the argument. - Jason Stajich

oh yeah, what Brad said, now that I am reading backwards! - Jason Stajich

Andrew Su

Would you call DAS a communication protocol or a data format? (http://biodas.org/documen...)

October 16 - Comment - Like - Share

Pierre Lindenbaum and Deepak Singh liked this

It's not a protocol in my book - Deepak Singh from iPhone

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False choice. Calling it a "service" might be more fitting (it has both a protocol and a data format). - Shiran Pasternak

Shiran, then you would say DAS (service) = HTTP/SOAP (protocol) + XML (format)? - Andrew Su

That's pretty much what all web services are aren't they? REST/SOAP + XML/JSON - Deepak Singh

DAS is a layer on top of these standards. The protocol describes how a client defines object types (e.g., genes) and coordinate slices; The data format describes how the results are represented in XML. - Shiran Pasternak

@Shiron does DAS really defines what is the type of object ? I mean, is "gene" a simple word or is it a component of an ontology ? - Pierre Lindenbaum

@Pierre DAS only defines "feature" as a type. There is no sequence ontology (not last time I looked). But it's up to the provider to define the interface so that a client can request meaningful objects like "genes" (or "pierres," for all it cares). - Shiran Pasternak

thanks - Pierre Lindenbaum

thanks all for the comments. Personally I think this is largely semantics, but I suppose if we talk about it in a paper the semantics should be right... - Andrew Su

Jo Badge

Just been into google wave and now I know why everyone is asking if people can see their wave. I am massively confused and befuddled, talking to myself is not good !

October 16 - Comment - Like - Share

Egon Willighagen, Cameron Neylon and Pierre Lindenbaum liked this

It's like entering an entertainment party... there is so much to see, to do, and to play with, that you're just confused about where to start... that's common with new things. Nothing to worry about. - Egon Willighagen

3 more comments

... the party analogy works on multiple levels. I feel like the schmuck sitting on the curb watching the cool kids across the street entering that raging party... flashbacks to high school... ;) - Andrew Su

Jo, have added you to a few waves at least - hope that helps - but I, having finally got home, seriously need to go to bed. - Cameron Neylon

Most excellent. Since you've got a week off with nothing to do, you can be our resident wave expert when you get back :-) - AJCann

Thanks guys! @cameron I'll go and play tonight (supposed to be holiday this week but leaves time for playing!!) @ajcann hmmm if u want a befuddled expert you've come to the right place. I'll be the one on the lounge when everyone else is in the kitch at the wave part. :-)) - Jo Badge from iPod

Andrew Su

why does blogger.com's preview feature suck so much?

October 15 - Comment - Like - Share

What's the problem ? - Pierre Lindenbaum

2 more comments

the "preview" button is only fake preview. It takes out the formatting tags but it doesn't show the post how it will end up on the blog. My guess is that it doesn't apply the theme's CSS? Anyway, makes fine-tuning (e.g., picture widths, background colors) rather difficult... - Andrew Su

Ah, OK, you're right, it doesn't apply the CSS style. I write my post with an external editor and I check the style in FF. - Pierre Lindenbaum

not sure I understand... when you check the style in FF, you are actually able to apply the CSS somehow? Right now I guess settings and hope for the best... (and then tweak after it goes live) - Andrew Su

Andrew Su

Favor: would you tell me if http://biogps.gnf.org is live for you? If not, where are you located?

October 15 - Comment - Like - Share

OK for me. France. 17H42 - Pierre Lindenbaum

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I wasn't able to connect yesterday from Rockville, and for the past day, http://downforeveryoneorjustme.com/biogps... reports we're down. But no other users are reporting issues, and we can't reproduce through all other means we have... - Andrew Su

Fine here. UK, 1643. - Simon Cockell

hmmm, apparently BioGPS returns a 400 error to HEAD requests, which is what that site looks for. so probably a false alarm then. Thanks Pierre and Simon... - Andrew Su

Andrew Su

I'm returning to San Diego today. - http://www.dopplr.com/travell...

October 14 - Comment - Like - Share

See more in my Dopplr profile. - Andrew Su

John Hogenesch

Am Google waving on a science project now. Wave seems a cross between Gmail and Basecamp. Robots are cool. Has promise, but definitely a learning curve.

October 13 - Comment - Like - Share

in case you hadn't seen it... http://ff.im/9GEor - Andrew Su

Pierre Lindenbaum

My contribution to Wikipedia - http://plindenbaum.blogspot.com/2009...

October 13 from YOKOFAKUN - Comment - Like - Share

Steve Koch, Andrew Su, Yann Abraham and 3 other people liked this

I spotted several duplicates and talk pages too... - Egon Willighagen

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Yes, that's why I said my 'count' was lower than those ~165 entries. :-) - Pierre Lindenbaum

How did you compile the list? Wondering what my count is... not created so much as you, and still am impressed by your productivity... even if 165 is the upper limit :) - Egon Willighagen

@Egon I used the wikipedia API to get my contributions: http://en.wikipedia.org/w... . Creating an article is actually fast thanks to my friefox/WP extension: http://tinyurl.com/9druf2 and a xslt stylesheet pubmed2wiki: http://code.google.com/p... . Biographies are found using this pubmed query http://tinyurl.com/ygsuz38 - Pierre Lindenbaum

Pierre's secrets revealed! - Andrew Su

Todd Harris

The (im)permanance of online biological resources - http://toddharris.net/blog...

October 12 from Todd Harris - Comment - Like - Share

Andrew Su, Tom.Pasley and Pierre Lindenbaum liked this

This has always been an issue, outside of any specific discipline... it would be good to have someone host a virtual image which was a production snapshot for interested parties to download, and run as needed. - Tom.Pasley

2 more comments

Personally, I think not every app should be actively maintained. Some tools (many/most?) deserve to gracefully fall away into obscurity if they aren't being used. it just doesn't make sense to maintain them, and it increases the cruft that end users have to sort through to find the best tools. OTOH, if you're getting _lots_ of requests and feedback, then I think that would be motivation to find continued funding. Having said all that, the VM idea is a pretty good one... - Andrew Su

Andrew - Good point. Sustained demand for a resource makes a good case for at least maintenance levels of funding. And I agree - there is a huge amount of noise with circulation of old tools and info (like Googling a problem and getting results from 2007 - always suspect). Still, so many bioinformatics projects generate resources and not always publications. It seems like we need a place to archive this content. - Todd Harris

@Tom You're right. And I'm certain that other fields have already made in-roads in this area. Would be good to leverage that experience. - Todd Harris

Allyson Lister

Woo-hoo - I made Google Wave crash Firefox :)

October 12 - Comment - Like - Share

Stability aside, I've heard that wave is _much_ faster in chrome. (Of course, just hearsay since I don't have an account yet. Wink wink in case anyone's got an invite to give...) - Andrew Su from fftogo

Wish I had invites - but I don't :( I just made it crash a second time. Might install Iron tomorrow and see how that goes... thanks for the tip - Allyson Lister

Andrew Su

I'm starting a trip to Bethesda today. - http://www.dopplr.com/travell...

October 12 - Comment - Like - Share

I'll be there from October 12th until October 14th. See more in my Dopplr profile. - Andrew Su

reflection to The Life Scientists, Biology

The 2009 Nobel Prize in Physiology or Medicine has been awarded for the discovery "how chromosomes are protected by telomeres and the enzyme telomerase" published in 1982. It was not mentioned that the theory of telomere shortening was published a decade before by Olovnikov http://www.youtube.com/watch...

Olovnikov1973.pdf 632 KB

October 6 - Comment - Like - Share

Ricardo Almeida, Nils Reinton and Alexey liked this

interesting & who is the person behind 'reflection'? Maybe that person knows Olovnikov himself. http://en.wikipedia.org/wiki... - Attila Csordas

11 more comments

Is not it strange, that a person who is well-known as the author of the telomere theory is not even mentioned? He was nominated for the Nobel prize as well, so he could have been at least acknowledged. It means that doing theory is not rewarding? - reflection

Agreed, this is strange. But it is typical of the Nobel process, which wants to make superstars and doesn't have much to do with actual science, and so it ignores the complex connections that actually drive discovery. Look at the Chemistry prize for "discovery of GFP" that went to three people OTHER than the actual discoverer. - Bill Hooker

IMHO, Nobels should be granted for sustained and conclusive work in a field, so personally, I think they got it right... http://www.ncbi.nlm.nih.gov/sites...] - Andrew Su

Interesting that the wikipedia article was started today. Unless that was one of you... - Jason Winget

Bill, but I associate GFP with those other three people who really brought that to fruition. That's fine by me. In other words I agree with Andrew - Deepak Singh

Actually I'm not even right about who *discovered* GFP... Shimomura found the protein, 20 years later Prasher cloned the gene. I still think Prasher got ripped off though, since it was only a couple of years after he made the clone available that it started to be widely used as a tag, whereas the protein was known for 20 years before that and no one could do anything with it. Not that... more... - Bill Hooker

I am thinking about the 1962 Nobel prize for the discovery of the molecular structure of DNA. The prize was awarded to the people who did theory. But that seems to be the only exception. Other than that, all prizes were awarded to the experimentalists. - reflection

Also remember that it took till 1962 to award the prize because otherwise there would have been four. The issues over that were only resolved when Rosalind Franklin died because the prize is never given posthomously. In the case of DNA you might argue that Wilkins was the experimentalist of course - Cameron Neylon

Interesting... from the book of Stephen S. Hall: "Cell paper confirmed the existence of telomerase and opened the door to one of the most productive areas of research in modern cell biology. It also confirmed Olovnikov's original hypotheses, but his train stil didn't arrive at the station, because Blackburn and Greider failed to mention his earlier theoretical work in their paper. "We... more... - reflection

"typical of the Nobel process, which wants to make superstars and doesn't have much to do with actual science".....hmmm......interesting perspective. Anyway, while discussing who was left out because of the three rule, S. Moncada is a recent one (NO). - Maxine

Maxine, my take on this is, the people who got it usually deserved it, and we should begrudge them their efforts. What we need to make sure is that deserving folks don't get left out. The three rule is tough one especially when big science comes into play. - Deepak Singh

Just as well science isn't literature or "peace" (aka politics!), where far more subjective elements come into play and the emotional reactions to the prizewinners seem to be far more extreme. - Maxine

Andrew Su

"Why don't you contribute to Wikipedia?" -- please share your answer, or common answers you hear from others

October 9 - Comment - Like - Share

Andrew Perry, Daniel Mietchen, Cameron Neylon and Pierre Lindenbaum liked this

The gripe I usually hear from academics is "I made edit X, but someone else undid it or [worse] edited it and changed it!". I'm usually thinking 2 things when I hear this "It's Wikipedia! If you really think your version was better then revert!" and "Do you moan like this when a co-author does this on an article?". - Paul Gardner

6 more comments

Paul - I think there is a bit of a deeper issue here that academics expect their authority on a subject to flow from the academy easily into the environment of Wikipedia. Never even occurs us to question whether or how this should happen. Need to realise that we need to earn that authority in a new environment. Which leads to my answer. I don't have the time to do the hard yards to earn... more... - Cameron Neylon

Once, one of my blog post about "the Scope trial" was used as the main source for the French article of wikipedia on the subject. One guy just took my post, somehow rephrased it, completed it a little bit, and referred to my blog as a source. I found that quite interesting, I wrote a blog post about it and on the relationships between wikipedia and science blogs. Then another guy read... more... - Tom Roud

I completely agree with Cameron and Tom. As a scientist, I am simply not willing to invest time in a community where authority has to be established independently of authority in the scientific community, where things I write may be deleted by people who have no authority on the topic in question within the scientific community, and where I in return get no credit or attribution for what I have done. - Lars Juhl Jensen

I contribute a few edits per month at the Wikipedias but many more on Citizendium. Why? Because the latter, although it has other drawbacks, shortens the mileage experts have to go to earn and exercise subject matter authority in such a wiki environment. Speaking of which, it is currently in a transition period in terms of governance (... more... - Daniel Mietchen

Pretty much what everyone else said. Wikipedia is thoroughly confused when it comes to authority -- they accept sources they should not and refuse sources they should welcome. I like and use wikipedia but (although I have done a couple of small edits and will continue to add things that don't cost me a lot of work), it's just not worth my time to wade through their editorial policies until those policies are at least internally consistent. - Bill Hooker

I have a short list of articles that I intend to work on or add, but haven't acted much yet - the bureaucracy scares me off. Like others, I make minor edits, but have never found the time to wade through all the documentation such that I would be confident in submitting a large piece of original work. I would actually like to do some sort of two day course (or have some mentorship) in... more... - Andrew Perry

Great answers, thanks all. If I had to boil it down to a few key phrases, I'm hearing these reasons so far: lack of authority as a scientist (or inability to transfer authority from the the academic world), lack of attribution/incentive, apprehension over policies and bureaucracy. More thoughts or clarifications are welcome... - Andrew Su

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