 |
|
| FriendFeed is the easiest way to share online. Learn more » |
Abhishek Tiwari › Comments
I need some feedback/career advice.
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
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
Warren DeLano of PyMol fame has passed away :(
Oh no, that's terrible news... how did you hear??
- Shirley Wu
on the ccp4 mailing list
- Deepak Singh
from IM
:(
- Rajarshi Guha
Very sad, I saw Warren introduce an early version of PyMol, it was an excellent piece of software for a one man effort. The mailing list announcement is here: https://www.jiscmail.ac.uk/cgi-bin...
- Greg Tyrelle
Ah i see. Nothing on the google yet. He was relatively young too, wasn't he? Sad...
- Shirley Wu
from twhirl
I met him in August and he seemed fine! very depressing
- Rajarshi Guha
:(
- Ruchira S. Datta
He wasn't much older than me and I knew him a bit back in my modeling days, so this really sucks
- Deepak Singh
Very, very sad. Today in my graduate course on RNA one of the students spent most of the class showing us images of the ribosome that he generated with PyMol. The first thing I introduce to the students in this course is how to use PyMol. This is truly a great loss to the community.
- Tom Tullius
so sad. I only interacted with Warren via email, but it was always a pleasure. I greatly admired his support of FOSS, and was inspired by his ground-breaking work in molecular visualization. such sad news.
- tim
Very sad news indeed... :(
- Egon Willighagen
:-(
- Michael Kuhn
this is a big and shocking loss
- Wladimir Labeikovsky
Wow. I met with him a couple of times. Very, very sad. It will be hard to use pymol now without thinking of him.
- Iddo Friedberg
Very sad. Condolences to his family and friends.
- Neil Saunders
Very sad indeed. His legacy lives on in awesome molecular graphics now and forever.
- Adam Kraut
Oh, that's really, really sad news :(
- Andrew Perry
It was a kick in the head today when I heard that he had passed. A sad day indeed
- Antony Williams
:-(
- Mickey Kosloff
So sad--young guy, met him at a conference about 2 years ago. Accomplished so much--his science and entrepreneurship was an inspiration to me.
- Mary Canady
Anyone else interested in helping continue the PyMol codebase?
- Donnie Berkholz
Donnie, certain hope that it doesn't go away
- Deepak Singh
Last I glanced at the PyMol codebase it was actually pretty scary. Sloccount says: Totals grouped by language (dominant language first): ansic: 477951 (85.93%) python: 65182 (11.72%) cpp: 12928 (2.32%)
- Anders Norgaard
I realize I might get slapped for this but with light comes shadow (very Jungian I know). The upside of Warren releasing code as Open Source is that his work can live on and be continued. This is brilliant. The shadow is what about about his young wife that he has left behind? I talked with Warren earlier this year and PyMol was helping him to create a living. But what does his family...
more...
- Antony Williams
Please drop your comments here http://warrendelano.blogspot.com/2009...
- Abhishek Tiwari
Babies' Language Learning Starts From The Womb http://www.sciencedaily.com/release...
"From their very first days, newborns' cries already bear the mark of the language their parents speak, reveals a new study published online on November 5th in Current Biology, a Cell Press publication. The findings suggest that infants begin picking up elements of what will be their first language in the womb, and certainly long before their first babble or coo."
- Ruchira S. Datta
Something resembles to Abhimanyu's experience in Mahabharat
- Abhishek Tiwari
"Hormone That Affects Finger Length Key To Social Behavior" http://www.sciencedaily.com/release... [I wonder which finger]
2D:4D ratio, also called Digit ratio http://en.wikipedia.org/wiki...
- Abhishek Tiwari
Data driven science: Evidence is not enough http://poolingideas.abhishek-t...
Neil Saunders and Deepak Singh liked this
Possibly for good reason. As Cosma Shalizi points out in Often Wrong, Never In Doubt http://cscs.umich.edu/~crshal... and Bayes < Darwin-Wallace http://cscs.umich.edu/~crshal..., Bayesian methods can infer the wrong model with 100% confidence.
- Ruchira S. Datta
Thanks Ruchira, fairly interesting links
- Abhishek Tiwari
Seems to me there's a wide expanse between using algorithms to both ask and answer questions and purely human-led effort.
- Mr. Gunn
The END of THEORY/HYPOTHESIS, not yet
- Abhishek Tiwari
Not for a long long time
- Deepak Singh
Fifty Years of Scientific History For You. In the Pipeline: - http://pipeline.corante.com/archive...
Jesper Lind, Ola, Itachi and Garret McMahon liked this
Can literature analysis identify innovation drivers in drug discovery? http://dx.doi.org/10...
- Abhishek Tiwari
from Bookmarklet
A Simple Cipher Governs DNA Recognition by TAL Effectors - http://www.sciencemag.org/cgi...
Mr. Gunn, Richard Badge and Steve Koch liked this
"TAL effectors of plant pathogenic bacteria in the genus Xanthomonas bind host DNA and activate genes that contribute to disease or turn on defense. Target specificity depends on an effector-variable number of typically 34 amino acid repeats, but the mechanism of recognition is not understood. We show that a repeat-variable pair of residues specifies the nucleotides in the target site, one pair to one nucleotide, with no apparent context dependence. Our finding represents a novel mechanism for protein-DNA recognition that explains TAL effector specificity, enables target site prediction, and opens prospects for use of TAL effectors in research and biotechnology."
- Abhishek Tiwari
from Bookmarklet
Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors http://dx.doi.org/10...
- Abhishek Tiwari
Will have to read this one- interested in how "context independance" was tested...
- Richard Badge
from Nambu
RT @kehan Brilliant visualisation of the scale of biology http://learn.genetics.utah.edu/content...
David Bradley, Simon Cockell, Anna Croft and 7 other people liked this
Nice and simple
- François Dongier
great!
- Abhishek Tiwari
Brilliant.
- Bill Hooker
Totally awesome!
- Björn Brembs
Upshot from 3rd CDD Community Meeting - http://researchscorecard.com/blog...
Jean-Claude Bradley, Michael Barton and Deepak Singh liked this
"Consequently, I’ve now officially joined the ranks of believers in Ruby on Rails (RR), at least when it comes to scientific software."
- Rich Apodaca
fanboy (OK, a bit harsh, but seriously, it's not like there hasn't been well developed scientific software)
- Rajarshi Guha
@Rajarshi, haha. Funny thing is, it looks like the author is not a developer. Seems that the positive RoR vibe is coming from a comparison of past experience with scientific software as a user/scientist, and the way CDD has implemented their system. I suspect a lot of this just has to do with working with a Web app done right, as opposed to anything Rails does in particular. OTOH, spending less time on infrastructure means more time for improving the user experience.
- Rich Apodaca
@Rich, good points. But my initial reaction was based on his statement that he worked in sci s/w - I'd have expected such a person to be a little more balanced. Another statement that made me raise my eyebrows - "RR is as big a step-up in facilitating the development of bio- and chemoinformatics software as Perl was in the early ’90s" - seriously, it's not as if there aren't...
more...
- Rajarshi Guha
It should also be noted that CDD is built on other people's cheminformatics tools on the backend. For example, ChemAxon's structure/substructure searching. I think that the backend tools should also be recognized in such commentaries by the original poster...I am assuming that they were discussed during the meeting.
- Antony Williams
@Rajarshi, I agree that the comparison may seem overstated. OTOH I don't agree with the idea that Rails is just doing what other Web frameworks do. True - there are many Web frameworks out there - but very few get it right. Just to clarify - are you saying it's CDD that's limited beyond its niche - or Rails? How so?
- Rich Apodaca
@Tony, I agree that the underlying tools play a big role in framing the capabilities of the resulting system. I think it would be very interesting for CDD to frankly discuss their experiences with ChemAxon's tools through non-traditional channels - for example, on their blog. I also think a similar discussion would be of value re ChemSpider, and any other public-facing chemistry database.
- Rich Apodaca
I was referring to CDD
- Rajarshi Guha
I have ignored CDD so far, because of the use of proprietary tools where one could do the same thing with open/free tools already... is there a compelling reason why I should be looking at CDD?
- Egon Willighagen
I think the main attraction of CDD is that someone has put together the system that is relatively usable. Granted, the capabilities are not particularly novel (and IMO, limiting for anybody but bench chemists who wish to just view/download/upload data) - but it is a nice interface
- Rajarshi Guha
So, what are the features that make it relative usable that other offerings do not have? In particularly, regarding cheminformatics?
- Egon Willighagen
I'm not aware of other offerings that have a focus on usability. I suppose PubChem could be one, but its interface sucks. I also would say that the access control (i.e. sharing) features are nice and I haven't seen that elsewhere. But yes, this could all be done pretty easily with a full OSS stack, it's just that nobody has done it (but I'm happy to be corrected!). But beyond that I...
more...
- Rajarshi Guha
@Egon, that's a great question (the one about features that make CDD more usable) that I'd hope current users of CDD could expand on.
- Rich Apodaca
I have used CDD as free user and found nothing special about CDD experience, may be because it is meant for the experimental and HTS scientist who can not do programming otherwise why you will go for such a interface. I will also remind that this is not a first application of its kind for example GVK Bio has also offering similar product although it is built on J2EE with ChemoAxon...
more...
- Abhishek Tiwari
Came across BioRails (http://www.biorails.org/wiki...) which looks nice. Has anybody used it?
- Rajarshi Guha
@Rajarashi, I'd be pleased to introduce you to some people who are using BioRails. I'd like to encourage more people to look at the open version. It has a strong workflow component and can be interfaced to tools like Knime and PP through its web service interface. We've used the Rail plugin architecture to integrate chemistry tools such as ChemWriter, Chemaxon, Accord and Symyx tools.
- Andrew Lemon
As for Rails, I can only say its been extremely productive, we have produced an extensive scalable application in a fraction of the time it would have required with other technology with a relatively small team. I'm not the one who did it so I'll leave it at that perspective.
- Andrew Lemon
Hi folks, CDD VP of Software here. Thanks for the discussion, though the remarks about Yannick (the blog author) were off, a little more care (maybe a google search) might be warranted there. His enthusiasm (read the paragraph before the quote) was inspired not just by Rails, but by CDD's software process, which I discussed a bit in my presentation at the meeting. And he's right: There...
more...
- Moses Hohman
@Egon To date CDD has not focused on users like you and Rajarshi (expert computational chemists/cheminformaticists), so I don't think there is much reason for you to pay attention yet. Our company's goal is to facilitate the growth of a community of data and people. The first step is getting people to contribute (privately or publicly, as they wish) their data, and for this usability...
more...
- Moses Hohman
@Rajarshi You're right that what CDD has done can be done with an OSS stack (other than ChemAxon we have done so), although I'm not sure that what CDD has done could be done *easily* ; ) We have spent significant effort. Some of the things on which we've spent the most effort aren't immediately apparent but are very important. The time it takes to build a user interface is famously...
more...
- Moses Hohman
Moses, can you elaborate on the things which would take considerable more time with an OSS stack? Who are your providers that make things so easy with your stack? OSS developers can't make GUI design easier, but surely can make a lot of other things easier. Like validating input.
- Egon Willighagen
Egon: I didn't mean to imply in my last post that things would take more time with an OSS stack. I just meant that, in general, what we've done took a lot of effort, and couldn't be redone easily (for some suitable definition of easy) with any stack : ) We use an OSS stack except for ChemAxon. Or maybe I don't understand your question? Are you asking why we use ChemAxon instead of CDK or something else? Or are you asking why CDD Vault itself isn't open source?
- Moses Hohman
I am trying to make a list of wave robots and gadgets that I have tried.
Please feel free to add list of robots and gadgets (or links) that you have tried, tested or heard with a one line description.
Paul Bacchus, Carl Fulp, Laura Norvig and 12 other people liked this
Gadgets: Add equation - to add equations to a wave Map Gadget : to embedd a map in to a wave Yes/No/May be Gadget - to add a quick poll to a wave
- Khader Shameer
Robots: calcbot@appspot.com - Do some easy calculations inside a wave bitly-bot@appspot.com - Add bit.ly functionality to a wave emoticonbot@appspot.com - Add emotions to your wave easypublic@appspot.com - makes the wave public tweety-wave@appspot.com - tweet from wave wavehangman@appspot.com - self-explanatory :) embeddy@appspot.com - generates HTML to embed the wave on any page (useful for getting the (globally unique) Wave ID as well) elizarobot@appspot.com - a chat bot
- Khader Shameer
Thanks to @sparkymat for sharing his list of Robots.
- Khader Shameer
helpmeigor@appspot.com reference management, janey-robot@appspot.com interface to journal name author disambiguation service. Though off topic, we are arranging a science wave hackday in london (http://blogs.nature.com/wp...), search for waves with the tag "swlhd" and you'll find us. The source for both of these is available, http://github.com/IanMulv... and http://code.google.com/p...
- Ian Mulvany
are the source codes available for any of these robots? thanks for sharing the list!
- Mike Chelen
http://techpp.com/2009... - ultimate list of Google wave robots and gadgets
- Khader Shameer
http://sites.google.com/site... - The official Google Wave extension list
- Khader Shameer
Hi Mike. My first stab source code can be found here... http://mcisb.svn.sourceforge.net/viewvc... Source code is also available for the emoticonbot somewhere, too.
- Neil Swainston
Neil, cool thanks!
- Mike Chelen
Here goes blast, synthetic biology and other science robots http://www.abhishek-tiwari.com/2009...
- Abhishek Tiwari
synbiowave looks fun, and it is on sourceforge http://sourceforge.net/project...
- Mike Chelen
Khader, thanks for starting this list. I have been compiling bots and gadgets here: http://j.mp/gw-bots as well, I think the only one not on this this is sweepy-wave@appspot.com that removes empty blip waves. I hope everyone feel free to contribute to the site I started, because like this list, it is meant to grow and serve as a resource for the wave community.
- Justin H. Johnson
Justin, thanks for sharing the details about the resource.
- Khader Shameer
IntelliJ IDEA :: The Best Java IDE Now Free and Open Source - http://www.jetbrains.com/idea...
Rajarshi Guha liked this
"We believe IntelliJ IDEA to be the best Java IDE on the market — and the world will only gain if more people start using it. That's why we decided to remove the main barrier — the price tag, and introduce the upcoming version 9 in two editions."
- Abhishek Tiwari
from Bookmarklet
Could we have a list of google wave names somewhere so that I can figure out what Life-Scientists are on there?
Tom Tullius, Jeannette Høvring, Daniel Jurczak and 21 other people liked this
toddwharris@googlewave.com
- Todd Harris
just added you to Life Scientists wave
- Cameron Neylon
from twhirl
A Google Wave might be appropriate for tracking such a group.
- Shiran Pasternak
shiranpasternak at the same domain.
- Shiran Pasternak
search "with:public research" and you will find the "Research collaborations in Wave" wave endre.sebestyen@googlewave.com
- Endre Sebestyen
yann.abraham@googlewave.com
- Yann Abraham
Searching Google Wave with "tag:the-life-scientists" will get you to "Research collaborations in Wave", a good starting point for life scientists.
- Martin Fenner
b.brembs@googlewave.com
- Björn Brembs
mndoci
- Deepak Singh
I also missed out on the invites .. if anyone knows someone .. :)
- Pedro Beltrao
I'm firstname.lastname
- Ruchira S. Datta
firstname.lastname here too
- Andrew Clegg
I don't get how you search in public waves. I've tried searching for tag:the-life-scientists and it gets no hits -- I think it's just searching my own waves
- Andrew Clegg
there was a thread by Kol about wave usernames couldn't find the link
- ffcode
Aha -- with:public . They really should include a button for that
- Andrew Clegg
anna.k.croft
- Anna Croft
Lots here: http://ff.im/91NZC
- Kol Tregaskes
thanks Kol
- ffcode
attilacsordas
- Attila Csordas
I never got invited to the party :(
- Lars Juhl Jensen
AndrewJamesPerry
- Andrew Perry
avijitguharoy@googlewave.com
- A Roy
allyson.lurena@googlewave.com
- Allyson Lister
@Endre: You can link to waves, eg: https://wave.google.com/wave...
- Nick Lothian
mbembee@googlewave.com
- embee
000.cacarr@googlewave.com
- Christopher A Carr
cassjohnston
- Cass Johnston
plindenbaum
- Pierre Lindenbaum
firstname.lastname också
- Egon Willighagen
diegomorelli76@googlevave.com
- diego morelli
abhishek.twr@googlevave.com
- Abhishek Tiwari
Would like to be added to life scientists wave, please! david.rothman@googlewave.com
- David Rothman (☤)
@David: done
- Pierre Lindenbaum
Many thanks, Pierre. :)
- David Rothman (☤)
churchsg
- Sally Church
life scientists wave: me too, thx
- Attila Csordas
Count me in: matt.j.wood
- Matt Wood
jeanclaude.bradley at googlewave dot com
- Jean-Claude Bradley
chrisamiller@googlewave.com
- Chris Miller
inspiring2designllc@googlewave.com
- Justin H. Johnson
somebody please add me too attilacsordasat...
- Attila Csordas
Attila: can't seem to find attilacsordas@googlewave.com.
- Shiran Pasternak
it does exist I can tell ya :)
- Attila Csordas
@Attila: tried a different way... yer in.
- Shiran Pasternak
An undergraduate student in our lab, Caleb, just got his wave invite. I told him to look at this thread for possible people to connect with.
- Steve Koch
+1 skhadar@googlewave.com
- Khader Shameer
got it, thanks
- Attila Csordas
murvine - thanks!
- Christopher Murvine
Afternoon all. I've written my first robot, which hopefully will embed an interactive mass spectrum into a blip whenever a UniProt name is encountered in the text, and corresponding mass spec data is found for this protein. I say "hopefully", as I've not been able to test it for real, as, alas, I have no account. When are the next batches released? If it's not for ages, does anyone fancy testing it anyway?
- Neil Swainston
Am now Waving as ben.blackburne.
- Ben Blackburne
Now waving as lars.juhl.jensen
- Lars Juhl Jensen
waving too: sciphu@googlewave.com
- Nils Reinton
waving as fgibson
- Frank
aemonten@googlewave.com. How can I get started with the life scientists wave?
- Alejandro Montenegro
my wave ID: macmanes@googlewave.com
- Matthew MacManes
dan.swan@googlewave.com searching is sloooooow trying to find the life scientists wave right now!
- Daniel Swan
chris.lasher@googlewave.com
- Chris Lasher
sjcockell@googlewave.com
- Simon Cockell
jwhabig@googlewave.com - Jeff Habig
- Jeff Habig
comprendia[at]googlewave[dot]com Mary Canady
- Mary Canady
rebeldad@googlewave.com Brian Reid (PR guy for life science types ... I promise to behave)
- Brian Reid
bronxman
- Jack H. Pincus
I'm trying to get a Solexa/Illumina Sequencing Wave going. Search "with:public Illumina" or add me macmanes@googlewave.com
- Matthew MacManes
waving as georgkam
- george
For some reason, I'm stevekoch3 but glad to finally have a preview account!
- Steve Koch
And I found the research collaborations wave by the following search: "with:public tag:the-life-scientists"
- Steve Koch
mine is pedrobeltrao@googlewave.com (thanks to Mr Gunn)
- Pedro Beltrao
In case there is still someone with spare invitations: piotr.byzia at gmail.com
- Piotr Byzia
tom.sante@googlewave.com
- Tom
Im steelgraham7@googlewave.com
- Graham Steel
sametstalker@gmail.com
- Samet Güngören
michael.kuhn
- Michael Kuhn
Requesting for life scientists wave, abhishek.twr@googlevave.com thanks in advance
- Abhishek Tiwari
The usual, neilfws.
- Neil Saunders
now that I am finally on board: danjurczak@googlewave.com
- Daniel Jurczak
i'm mightyfib(at)gogglewave(dot)com Your most welcome to add me...:O)
- Jeannette Høvring
mine is dave.lunt
- Dave Lunt
michael.chelen@googlewave.com - seems to use the google contacts system like gmail
- Mike Chelen
pengwen.not.penguin@googlewave.com
- Parvez Halim
mstalnos@googlewave.com
- Tresterling
I'm on (thanks to Steve Koch!): tom.tullius@googlewave.com
- Tom Tullius
Which online notebook to use? Zotero, others? I just need some simple stuff, to write down ideas, links, keywords, short lists, etc.
Salvatore Loguercio, Steve, Justin H. Johnson and 9 other people liked this
For the 'large lists' I use Google Docs. I use a spiral-bound notebook to write down my ideas.
- Pierre Lindenbaum
I still think Google Notebook is (was) the best. I still use it, but you can't sign up anymore. Plenty of other options - Zoho (very similar), Evernote (for the iPhone crowd), Ubernote (OK but not so slick). Wikis are good for this purpose too - plenty of hosted options - Wikispaces, Wikidot.
- Neil Saunders
And i do have a Google Notebook account that I never used! We will see. Thx for the other hints too.
- Endre Sebestyen
google docs is good for collaboration and publication, especially with spreadsheets. zotero is great for managing journal citation and collection. for short notes, friendfeed works well
- Mike Chelen
I prefer local apps for this - don't want to be cut off from my notebook when I'm travelling or for some other reason not connected to the Net. Use Journler on the Mac (http://journler.com) for notes, and Things (http://culturedcode.com/things...) for tasks lists and jotting down ideas.
- 'Mummi' Thorisson
Mummi: google gears works pretty well for that suite
- Mike Chelen
yeah, I am somewhat dimly aware of the offline-access ability of those apps. Just haven't taken the plunge and really used them - e.g. haven't co-authored a document via Google Docs yet. That notwithstanding, I'm still sceptical about even an offline-capable Web tool for something as personal & critical as keeping notes. For collaboration, hell yes :)
- 'Mummi' Thorisson
problem with google gears is that it isn't working with firefox at the moment. btw emails are also really personal & critical and we still use gmail, etc :)
- Endre Sebestyen
Endre, it does if you go find a plugin built by someone else that's compatible with Firefox 3.5 and/or 64-bit (whatever your requirement is). I've got it going.
- Donnie Berkholz
@Endre - I use GMail also but via IMAP to my Mail app on the Mac, so I always have local copies of all my mail (one of them E-mail hoarders, you see: got tens of thousands messages stashed away...). But webmail access is good to have as a backup when not at my own 'puter.
- 'Mummi' Thorisson
Mummi: the things that are most critical to me are also most important to have online, because of the flexibility of access across desktops, laptops, and phone. imap is a great example of synchronizing between remote and local systems, currently using dropbox, wuala, or conduit (linux app) to do something similar with files
- Mike Chelen
I continue to be more drawn into Evernote--slowly using it more and more since I first downloaded maybe 1/2 a year ago. Works very well. Syncs local copies on multiple machines (and phones) with plenty of central storage space and works very well offline. Recently noticed shared notebook and public notebook features which are appealing. Still using free version -- paid version interesting if all lab members using it for open science (in the future).
- Steve Koch
Yeah Evernote all the way. I use it for meeting notes and lists (ctrl-shift-C gives a check box), works great offline. The iPhone app is getting less buggy with updates as well.
- Sarah Kendrew
I would try evernote, but it seems they don't have a client software for OSX 10.4 (i never upgraded somehow, maybe it is time). Well I'll start now with the web interface.
- Endre Sebestyen
Somehow I prefer Zoho writer as it has an Office plug-in which help me to synchronize from desktop version and inserting citations using Zotero plugin which currently you can not do with Google Docs.
- Abhishek Tiwari
Have a look on this image http://1.bp.blogspot.com/_K2PSkf...
- Abhishek Tiwari
@Mummi: Offline access -- particularly for mail -- works great! I finally dumped IMAP because of oddities moving between devices. I've even grown to appreciate the web interface over a full-fledged client for speed in archiving and deleting.
- Todd Harris
It's not really online, but Omnifocus is worth checking out: http://www.omnigroup.com/applica.... It is a GTD implementation without being too heavy-handed. It has an iPhone app that synchronizes with a desktop client. But I also agree with Pierre: Plain old notebooks, Moleskines at that.
- Todd Harris
Oh yes, Zotero is a great structured online/offline notebook. Never saw it that way because of the pre-defined structure. But yes, I would recommend Zotero as notebook and I am storing my notes in my private research folders all the time :) Zotero 2.n is also always good to share things in groups. Hint: Create a public group for yourself to have a kind of Zotero blog. Hint 2: Run the Zotero feed through FeedBurner which will automagically present the structure to subscribers.
- Markus Merz
Google docs with gears & zotero. If you're using Opera it has built in memo app that synchronizes across all Opera browsers. I'm just waiting for that zotero extension for Google chrome.
- Sung W. Lim
Evernote - works with my various PCs, it works with my blackberry and my wife's iPhone, heck it even works with pixily for scanned documents.
- Andreas Matern
Processing 1.0 - http://processing.org/
Processing is an open source programming language and environment for people who want to program images, animation, and interactions. It is used by students, artists, designers, researchers, and hobbyists for learning, prototyping, and production. It is created to teach fundamentals of computer programming within a visual context and to serve as a software sketchbook and professional production tool. Processing is an alternative to proprietary software tools in the same domain.
- Frank
+ProcessingJS http://processingjs.org/
- Abhishek Tiwari
Animated Transitions in Statistical Data Graphics - http://www.abhishek-tiwari.com/2009...
  |
Mr. Gunn, Hari, Marcos de Carvalho and 7 other people liked this
Now that's cool. But where can I get it?
- Cameron Neylon
very slick - I'm guessing from the presentation this is a commercial product?
- Jean-Claude Bradley
Although there is not much detail on the website but it is developed by Jeff Heer who also developed the Flare and Prefuse- both are open source. In fact he is one of authors of O'Reilly's Beautiful Data.
- Abhishek Tiwari
that would be great if it were OA - very impressive way to communicate - I could see it used at conferences
- Jean-Claude Bradley
in the meantime take this sizeable appetizer: http://oreilly.com/catalog...
- Claudia Koltzenburg
Chapter 7 of 'Beautiful Data' linked here http://friendfeed.com/guyl...
- Claudia Koltzenburg
Re: Mendeley to CiteULike and other CiteULike enhancements- by Fisheye Perspective - http://www.abhishek-tiwari.com/2009...
"I could not agree more, it should be "post" rather than "import"."
- Abhishek Tiwari
Practical RNA structure visualization with VARNA - http://bio-geeks.com/?p=686
Ruby Script
- Abhishek Tiwari
Its time for me to prepare a CV for my post-doc applications, any suggestions ? What are the must haves in a bioinfo post doc CV ?
Daniel Jurczak, Lucas Brouwers, Mike Chelen and 5 other people liked this
Focus on the position requirements, and do not add in minor stuff not required, unless where it serves as topic for the interview.
- Egon Willighagen
Keep it short. Use a template. Spelling/grammar errors look bad. Focus on the cover letter, not the CV. Say why you want the position and what you will bring to it - generic applications look very bad. Rather than listing skills, give examples of problems that you've faced and how your skill set solved them. Publications, presentations posters etc. can be a separate section in a smaller font, after the other stuff.
- Neil Saunders
Agree with both the above. You can tailor the CV itself to the job you're applying for -- don't have a one-size-fits-all. Emphasize different skills and experiences depending on where you're applying -- some could be left out for brevity in some job applications, but left in for others if they're more relevant. Plus it doesn't hurt to ask a slightly more senior friend or colleague if you could see theirs, to have something to work from.
- Andrew Clegg
Thanks Egon, Neil, Andrew for the different, yet important points.
- Khader Shameer
Agree with above about the cover letter. On the CV, one URL pointing to your publications (via citeUlike, zotero etc), another pointing to your LinkedIn profile.One URL for your blog. Restate your relevant skills, as appropriate for the job and thats about it.
- Frank
Pawel built nice tag cloud for his resume: http://www.flickr.com/photos...
- Pierre Lindenbaum
Frank: Do you think listing your pubs on your CV is out of date these days? Personally I think a link to a comprehensive online list would be better, but I'd worry about old-fashioned employers thinking that "wasn't the done thing". Also that puts the onus on the reader to actually fire up a browser and put the link in (esp. if it's a printed CV)
- Andrew Clegg
If it's a PDF CV, include links to the pubs?
- Rajarshi Guha
Frank : I am not yet an active blogger - is that an absolute requirement for a compbio postdoc or job :| ?
- Khader Shameer
I am planning to put a link to my publications in PubMed as suggested by Rajarshi, but some of them are conference abstracts / non-pubmed publications, so I need to use a combination of both.
- Khader Shameer
Don't forget to mention about you computational and programming skills in a detail, I guess most of Post-doc potions need programming skills well advance so just open up
- Abhishek Tiwari
Thanks Abhishek, will have a section dedicated to tech skills. But at the same time I don't want to enumerate n number of technologies / bioinfo tools am familiar with. That would easily fill 2 pages of my CV.
- Khader Shameer
Compliment @all. Nice crowd sourcing. Found via search for zotero. Trackback: http://identi.ca/notice...
- Markus Merz
@Andrew. I think it depends on the job, if you are going for a research position, they generally want to see what you have been doing, a non research position a reference list is probably irrelevant. I would agree that producing a list of your publications actually on the CV is outdated and would probably extend the page limit, I did suggest adding a link rather than listing them :). They would have to navigate to Pubmed to "read" them anyway.. or at least check the dates
- Frank
@Khader, wether you blog or not is your decision, I doubt it would be a deciding factor. I probably would expect to see some online activity, opensource project, link to research code, etc. However, I do understand this largely depends on the work you have actually been doing and is not a given
- Frank
Regarding publications: how about a handful of key relevant papers on the CV itself, plus link to full bibliography on one's website (w/ links to PubMed).?
- 'Mummi' Thorisson
Mummi: Dunno what Khader's CV is like, but if it was me applying for my first postdoc, those two lists would have been the same :-)
- Andrew Clegg
Frank, Mummi, Andrew - Thanks for the points. My thesis related papers are in different stages of review, so I may not be able to provide a link to full list of publication as of now. I am planning to provide list of publications within the CV as of now, once I get my papers accepted, I can substitute it with a link to PubMed. I think Chris Millers CV is a good template for an online CV http://www.chrisamiller.com/cv... . Now need to find one good template for an offline version.
- Khader Shameer
Thanks guys. Prepared my CV and cover letter with your suggestions and send the application yesterday. Today, I just finished my first post-doc interview. It was a nice experience.
- Khader Shameer
Publication list is the most important thing on a CV. One gets so many applicants, all of whom write their cvs so well, that one inevitably distinguishes between candidates on their publication record.
- Matthew Todd
Good luck, hope the news is good
- Andrew Clegg
Andrew, thanks ! It went on well - now waiting for the next steps : reco, thesis submission, etc.
- Khader Shameer
Bring Back Reprint Requests :The Scientist [2009-09-01] - http://www.the-scientist.com/article...
Donnie Berkholz liked this
"The Internet has changed scientific publishing in many ways, some good and some bad. No one would deny that it is easier to find papers on a particular subject than ever before. Looking up papers in Index Medicus or by browsing Current Contents has long been replaced by online searches on Medline or even Google Scholar. This has not necessarily improved our understanding of the literature, but it certainly provides a quick way to feel up to date."
- Abhishek Tiwari
from Bookmarklet
quick way to get rid of this pang of nostalgia: file and send the reprints yourself, don't have your secretary do it
- Wladimir Labeikovsky
on the other hand. maybe torrents of emails asking for pdfs will motivate the PI's that remain apathetic towards open access
- Wladimir Labeikovsky
I agree that the ability to track readership and download stats for my papers would be *extremely* valuable. It will probably just become more so as online papers approach the next-gen prototypes so you could even tell which sections and figures are viewed most.
- Donnie Berkholz
So discontinuous a discontinuity - http://futurememes.blogspot.com/2009...
Daniel Mietchen liked this
"A key aspect of thinking systemically about the future is being able to see how rapidly advancing technologies across many fields interrelate."
- Abhishek Tiwari
from Bookmarklet
Cold Summer, Hot Winter - http://initforthegold.blogspot.com/2009...
"Australia has experienced an extraordinarily hot winter."
- Abhishek Tiwari
from Bookmarklet
Timing is Everything :The Scientist-You want to be ahead of the curve, but not so far ahead that no one can see you. - http://www.the-scientist.com/2009...
Amira, Claudia Koltzenburg, Cameron Neylon and 2 other people liked this
"One of the most difficult questions a scientist must resolve is which problem to investigate. An especially critical aspect of this process is getting the timing right. When you start working on a new problem, it always takes time to get the experimental system working. Then you have to get your data, write it up, and publish. By this point, years can have gone by, and what was cutting edge when you started may have become passé."
- Abhishek Tiwari
from Bookmarklet
"It was hard to accept the thought that my research ideas were too innovative to be funded." - I think this is true way to often in our current system. Solution: make funding decisions in public, e.g. via http://fundscience.org/ .
- Daniel Mietchen
As Sydney Brenner wrote a couple of times: you want to be half a wavelength off in either direction ;)
- Wladimir Labeikovsky
As we discussed on c2cbio some episodes ago, most science is fundamentally incremental. People didn't go from elements to atoms in one day. It took a long long time.
- Deepak Singh
Wolfram Alpha to open data feeds | News | guardian.co.uk - http://www.guardian.co.uk/news...
Stylish Eve, Wladimir Labeikovsky, Daniel Mietchen and Mike Chelen liked this
"Wolfram Alpha, a project from the makers of math software Mathematica, will soon be opening up its data sets, opening up new possibilities for data mash ups"
- Abhishek Tiwari
from Bookmarklet
good, an API is exactly what it needs
- Mike Chelen
Fwd: A Quick Guide to Teaching R Programming to Computational Biology Students http://www.ploscompbiol.org/article... #rstats (via http://friendfeed.com/yannabr...)
Khader Shameer and Abhishek Tiwari liked this
Do check the supplementary material, very good tutorial out there
- Abhishek Tiwari
Just got news of a grant approval.
Neil Saunders, Jean-Claude Bradley, Björn Brembs and 14 other people liked this
Congratulations
- Jan Aerts
Always good news!
- Cameron Neylon
Thanks guys!
- Paulo Nuin
Congratulations Paulo
- Nils Reinton
Congrats! What will you be working on?
- Mr. Gunn
It's a grant typed as catalyst in Canada, focusing on the creation of collaborating teams. On this one we will study bladder cancer and biomarkers. More at http://webapps.cihr-irsc.gc.ca/cfdd...
- Paulo Nuin
Congratulations!
- Ricardo Vidal
from iPod
Congratulations! Collaborations FTW!
- Shirley Wu
from twhirl
That link doesn't work.
- Mr. Gunn
Try this one, and check the last entry http://webapps.cihr-irsc.gc.ca/cfdd...
- Paulo Nuin
Drinks are on Paulo ! Congratulations.
- Andrew Perry
Good work Paulo!
- Adam Kraut
congratulations! Beer o'clock will be hitting early!
- Kubke
Thanks again everyone.
- Paulo Nuin
Congratulations
- Abhishek Tiwari
Congrats !
- Khader Shameer
congratulations
- Frank
well done!
- Jean-Claude Bradley
Is there a best practice for microbial genome annotation?
Rob Syme, Mike Chelen, Pierre Lindenbaum and 6 other people liked this
Nope. There are a variety of pipelines that perform similar tasks. Good starting point might be IMG documentation - http://img.jgi.doe.gov/w....
- Neil Saunders
Worth remembering that there is very little "best practice" in any bioinformatics. For a long time, we made it up as we went along. It's only this new generation of bioinformaticians that have any formal software engineering education and bandy around fancy terms like "best practice" to make us feel bad ;-)
- Neil Saunders
I think its more like the Perl culture "There is more than one way to do it !!" Best practices in bioinformatics is currently in an ad-hoc state of practice.Just like Damian Conways's Perl Best Practices is one of the best guide for good coding practices for Perl - hope we will also have a book on "Best Practices in Bioinformatics" soon, may be by a group of authors from LifeScientists room - what say ?
- Khader Shameer
@Khader thats why we need flexible guidelines and not the constrained best practice. Several minimal guidelines have been already worked out for the different aspects of the life science domain. MIBBI (http://www.mibbi.org/index...) can be a good starting point in this case.
- Abhishek Tiwari
I think very often in bioinformatics, TIMTOWTDI. It's not like software development, with a "task" and an "optimal solution". What I think matters most is that however you do it, it's documented and repeatable.
- Neil Saunders
I completely agree with you Neil, but some efforts towards developing well defined, documented workflows / protocols (can we call this as "Best Practices") to perform generic tasks (eg. annotation) will be useful for the community. I think several 'standards' (eg. MIRIAM/MIBBI) are developed to bring in a common frame work for routine tasks. I believe TLS is an ideal place to get a consensus about such practices and work on a wikibook of best practices in bioinformatics.
- Khader Shameer
And I agree with you. I'm all for standards and best practice. I'm also a realist and a practical bioinformatician :-)
- Neil Saunders
@Abishek : Best practices are not always "constrained", and constrained practices are impossible due to complexity of biological system - flexibility should be there. But my point is that even if MIBBI / other standards (http://www.mibbi.org/index...) are available for a long time - I've never seen them in research papers - is it due to poor visibility of such projects or no interest in promoting such initiative ?
- Khader Shameer
Khader, that's a good question. There seems to be a disconnect between standards developers and the people who should be using the standards. I think it's a publishing problem. Developers publish in computational journals and use computational jargon; users don't read those journals or understand the jargon.
- Neil Saunders
Khader, In my opinion the main motive of guidelines is to avoid the disagreement while best practices try to bring an agreement in community. Also, people are using these guidelines. Its just lack of awareness otherwise more and more people will adopt them. Take any Biomodels database model or CellML repository model, they are well annotated according to MIRIAM guidelines. Allyson...
more...
- Abhishek Tiwari
I find the line "it's not like software development" to pretty much sum up some of the problems in bioinformatics. Why isn't it?!?
- Neil Swainston
It's complicated :-) In part, it's because researchers are more interested in quick answers (= quick fixes) than good code. In part because it's only in recent times that bioinformaticians receive formal software training. In part, because biological problems are more complex than input -> process -> output and you don't always know exactly what you want to achieve when you start. And I guess, biological information has a lot of "context", not easily captured by simple routines.
- Neil Saunders
Hi Neil. Yep, all that you say is true. Just from a personal perspective, I've found that being "disciplined" in writing code (making nice, clean, interfaces to modules, unit testing, documenting) means that in the middle-to-long-run, quick answers are easier to come by. By building up a reasonably reliable library of classes (I'm a Java-geek), sticking the bits of Lego together is...
more...
- Neil Swainston
Neil, I absolutely agree. It took me some time to get to the point of trying to "do things right" from the outset - libraries, documentation etc. and I'm glad I got there. I think a lot of the problems stem from how academic research is conducted. "Can you just give me a table by tomorrow?" "Sure, let me write a library." "No, I just want a table." Hack together perl script, deliver table, discard, move on. Rinse and repeat, until contract expires. Leave mess behind.
- Neil Saunders
Couldn't put it better myself! I guess I'm lucky in so far as that I do have the luxury of longer timescales... until my contract expires.
- Neil Swainston
Thanks Abishek for the pointers to application of different standards. My point is the goal of both best practices and standards are the same - getting a consensus to do repetitive experiments / workflows. But as Neil's are discussing - the choice of individual bioinformatics projects is mainly to get a good fix, rather than an excellent code base. But hope some degree of consensus can be obtained if people can follow standards as a first step.
- Khader Shameer
Science isn't set up to reward coding standards. Funding agencies reward quick biological results, not infrastructure and software development. I'd argue that for every 5 biological grants, the NIH should be funding one software/database/computational infrastructure grant. The amount of data is only getting bigger.
- Chris Miller
I'd agree with that, Chris. Career wise, it's pretty much immaterial whether I churn out a hack or something "good" and reusable. It's quite annoying. Grrrr!!
- Neil Swainston
@Michael / Neil : I am agreeing with "Science isn't set up to reward coding standards", but as a subject in the interface of science and technology - it is high time that bioinformatics should embrace the standards. For Michael's question I was trying to make a point that if there is a standard/best practice/generic protocol for microbial genome annotation - he could have just followed...
more...
- Khader Shameer
I think genome annotation is an excellent example of how bioinformatics is not like software development. You don't just run a program and annotate a genome. There are lots of biological features: protein-coding genes, non-protein coding genes, motifs - all with their own associated metadata, all with various, disparate tools written specifically for each type of feature. Annotation is...
more...
- Neil Saunders
too right Neil. is there a best practice for violin-making, vision quests, or coming-of-age experiences? ;)
- Ian Holmes
:-) Exactly. The end result is what matters.
- Neil Saunders
srsly tho -- there are plenty of papers describing microbial genome annotation. it's still an open research area, but there are commonalities (repeats, transposons, genes, typical errors, ...) so I guess the rough union of those vague concepts would constitute the current best practice. not exactly a recipe...
- Ian Holmes
:D best practice for violin-making, vision quests, or coming-of-age experiences :D - Neil, in the current era of bioinformatics with Webservices and Work-flows - having an SOP/BP is always help you to kick start the work in minimal time rather than going through all genome project paper for the flowcharts for annotations.
- Khader Shameer
@ Ian : OK, finally that's something that Michael/any one interested in annotation to get from this thread.
- Khader Shameer
Khader, what we're saying is that in this case, there isn't an SOP/BP, because it just isn't that kind of procedure. But there is, as Ian says, plenty of advice available. I guess, in terms that CS people might understand, it's not agile. You actually have to put some work into understanding what's going on and what you want to do.
- Neil Saunders
@Neil - ^(chicken|egg)? - It could and should be that kind of procedure though. All the advice in the world isn't going to help the people that actually *use* your annotations. The current 'system' for annotating anything is so mindlessly broken I'm surprised it works at all. Now all it needs is a catchy name. Blight of Bioinformatics maybe?
- Paul J. Davis
Thanks for the comments everyone. I'm going to read as many genome papers as possible and try and put what I read together.
- Michael Barton
Just remembered this article: http://www.nature.com/nbt... whic is a good look at current annotation practices. I also finally found http://www.ncbi.nlm.nih.gov/genomes... which describe's actual paramters that NCBI uses for gene prediction.
- Paul J. Davis
Neil Saunders, I agree a lot of advice is available and it is definitely helpful. For example, I was not aware of something like MIARE (thanks to Abishek), am now implementing in our RNAi screen. But I can't agree with you if you define bioinformatics projects as non-agile. From a simple BLAST based sequence analysis to large scale data analysis is following agile approach. Think of n...
more...
- Khader Shameer
Thanks Paul,for the links to the articles.
- Khader Shameer
Khader, your very use of the word "agile" sums up what this is all about. Clearly you are "new school" bioinformatics and appreciate software development. "Old school" bioinformatics would never even use the word :-) As I keep saying, I don't disagree with anyone here who calls for better practices, standards or "agility". Just be aware that there are still plenty of old-timers around for whom bioinformatics means "hack together something that works."
- Neil Saunders
Here's a paper that describes how microbes are annotated in Swiss-Prot: http://dx.doi.org/10...
- Eric Jain
Neil : Just loved the definition "hack together something that works" :)
- Khader Shameer
Summoning the FF hive-mind to give examples of fads in science. A fad is defined as a notion that is highly popular for a short term, although its popularity stems from the claim to be a long term or ultimate solution to whatever problem is being addressed. Discuss.
Mickey Kosloff and Mike Chelen liked this
cold fusion?
- D0r0th34
combinatorial chemistry?
- Deepak Singh
evolutionary psychology?
- Meg v. Meg v. 1.0.0.1
hype cycles ... http://pbeltrao.blogspot.com/2007...
- Pedro Beltrao
you need to update that. Personal genomics is way up on the hype cycle :)
- Deepak Singh
from IM
well it was in 2007 :) .. I should update it one of these days
- Pedro Beltrao
systems biology. (That said, these things always work in cycles - the overhyping, the cries of false promises, the retreat from the limelight, and the slow integration into the mainstream)
- Chris Miller
Chris, you have to look at Pedro's diagram then
- Deepak Singh
from IM
stem cells (oh snap!)
- Wladimir Labeikovsky
Grand Unified Theory, String Theory
- Sriks7
Super conductivity
- Sriks7
was string theory ever a fad? High Temperature superconducting, absolutely
- Deepak Singh
from IM
Genome-wide assoziation studies, fMRI
- Björn Brembs
from iPhone
leeches?
- Mike Chelen
I don't think HTS, GUTs or Strings can be called fads because they have been around too long for that. There are fads *within* those subjects for sure, but I think something that is popular for >20years is not a fad.
- Matt Leifer
fractals
- Jason Miller
chaos theory as a Rosetta stone for nature
- Jason Miller
Nostratic. Though I guess it was never that popular. Generative grammar, then.
- D0r0th34
Prions.
- Neil Saunders
wearing sandals in lab
- Mike Chelen
microarrays
- Mr. Gunn
snap-bracelets
- Mike Chelen
from IM
+1 Jason. Chaos and fractals. Also cellular automata (though all 3 are very interesting fads)
- Ian Holmes
Here's another good one that may be a bit more obscure: the catastrophe theory that was prostheletized by Zeeman. (Now, the mathematical theory of catastrophes is well established. The fad was to apply it to everything.)
- Jason Miller
Wow. nice thread. Now..muhahaha... you have helped write half of a new blog entry. TYVM. Especially Pedro.
- Iddo Friedberg
YOU_NAME_IT@home projects... or a bunch of crappy PCs contributing 24/7 to global warming.
- Martin Jambon
Not sure that some of these things are fads. I guess that the ultimate test for phenomenon being a fad is that it ends up being discarded, or adopted at a a much lower key than it was initially played with. Maybe a good test would be to look for historic NSF/NIH/DOE roadmaps, and see whether the highly funded projects and topics of a decade or two ago actually "made it".
- Iddo Friedberg
Open X Open Y Open Z
- Abhishek Tiwari
yes i forgot about catastrophe theory! nice one. Can we add category theory too?
- Ian Holmes
A bit outdated, but what about "solving the protein folding problem" or discovering a protein with a "novel 3D fold".
- Mickey Kosloff
Mickey - Your 'protein folding' wasn't such a fad as a 'much harder problem' than people thought. Many people are still working on it, and it will have a huge impact when solved.
- Jason Miller
I do maintain that "it's not rocket science" should be replaced with "it's not protein folding". Getting a ship to the moon's a lot easier problem to solve :)
- Deepak Singh
@Jason - my personal view is that current state of the art structure prediction approaches (which is what most people are working on) are not what people *used* to refer to as "solving the protein folding problem". More specifically, before the CASP experiments started people used to frequently publish papers that stated that they solved this problem (again). My impression is that CASPs seem to have killed that particular fad.
- Mickey Kosloff
Mickey, not the protein folding community (which is different from the structure prediction community). What happened was structure prediction got good enough and CASP (which I don't really like) gave people bragging rights, so that's where the effort went. Some day people will get back to real physics :)
- Deepak Singh
@deepak. What happened with CASP was that a lot crystallographers and biochemists got sick of theorists claiming that they had solved the protein folding "in principle", which would happen like clockwork every few months in the 90s. CASP was put together as a challenge to put your money where your mouth is. Unsurprisingly the claims of having solved the protein problem dropped significantly after the first CASP.
- Bosco Ho
from iPhone
@ Deepak. I agree with Bosco, and perhaps I wasn't clear enough in my initial comment. The fad I referred to was not studying protein folding (either experimentally or computationally), but the (frequent) declarations of solving the protein folding problem. This was before my time, but people that have been involved in CASPs since the 90s still remember this "fad" well. I participated...
more...
- Mickey Kosloff
From my recollection most of the physical folding people never even took part because all you could even try and look at were small models (people like Peter Wolynes and Dev Thirumalai). It was the comparative modeling/threading folks who were participating and trying to out CASP each other with entire labs shutting down for half the year. That's just bad science. I think the first few CASPs had a purpose, and with all the structures being solved made a lot of sense, but CASP outlived its use in about 2004.
- Deepak Singh
Now we're hijacking Iddo's thread for some CASP-bashing, which might require a separate thread (if not a separate room) :-)
- Mickey Kosloff
... lol true. Sorry Iddo
- Deepak Singh
from IM
Not that there's anything wrong with that (CASP-bashing, I mean).
- Mickey Kosloff
Structural Biology Rankings - http://www.molecularstructure.org/
Mickey Kosloff, Ruchira S. Datta and Nakao M. liked this
"Scoring of structures involves a simple equation in which the product of the total number of citation and the total number of downloads (scaled to not overwhelm the citation data) is divided by the squareroot of the number of days since the structure was released. The time-scaling ensures that older structures which have had time to accumulate more downloads and citations are not given an unfair advantage. The squareroot modifier ensures that newer structures are not given an unfair advantage due to the fact that citation and download rates have been increasing over time"
- Abhishek Tiwari
from Bookmarklet
New Algorithm, mrFAST, Counts Duplicated Regions in Personal Genomes - http://www.bio-itworld.com/news...
Khader Shameer and Ian Holmes liked this
The mrFAST algorithm has three major goals: first, to map large amounts of next-generation (short-read) sequence data to the reference genome; second, to determine the depth of reads across the genome; and finally, to identifying single nucleotide polymorphisms (SNPs) across the genome, including duplicated regions.
- Abhishek Tiwari
from Bookmarklet
Completely unrelated, but I sometimes wonder how much software/protein/protocol names are motivated by "wouldn't it be cool if our algorithm was called Mr. Fast!?"
- Benjamin Tseng
Benjamin that true although in this case mrFAST stands for “micro-read Fast Alignment Search Tool”
- Abhishek Tiwari
Your genome isn't that precious – give it away - opinion - 24 August 2009 - New Scientist - http://www.newscientist.com/article...
Mike Chelen, Jean-Claude Bradley, Vedran Rodic and 8 other people liked this
"Great scientific advances never come without risk, but more often than not hindsight shows us the risks are worth taking. When worrying about the safety of our genetic material, a little humility may be more valuable than musings on costs and benefits or sophisticated safeguards. As my astute father said when our family began sharing our 23andMe results: "I'm not worried. I'm just not that important.""
- Abhishek Tiwari
from Bookmarklet
I know I'm not important. But still worried :) Good essay to read, though, definitely swayed me more toward genetic / medical openness.
- Steve Koch
I've always felt that when I finally fork out to have my SNPs read I'd like to make the raw data freely available to anyone. I'd frankly be flattered if anyone even cared to look at it, and thrilled if it was in some way useful to someone beyond myself and my immediate family. My only concern is health insurance companies may use it to deny me (reasonably priced) service. The recent US...
more...
- Andrew Perry
It's something of a dilemma. If SNPs are not deterministic for diseases, then why bother having them analysed? If they are, then arguably, insurance companies are somewhat justified in denying me, knowing that I'm afflicted. A very simplistic view I know (a SNP may put you at increased risk, but that may be mitigated if you modify a behaviour). The problem with legislation is that simplistic often wins out over complex.
- Neil Saunders
I'm with Neil & Andrew. Even if the concerns aren't justified, it's pretty tough to _know_ they're not justified. Especially given the big parties -- govt. & insurance-- that are involved. At what point are you obligated to disclose pre-existing conditions when applying for insurance? (Legally; morally another question.) Of course the insurance company won't sue until there's $100K at stake. But those are the cases you're worried about.
- Steve Koch
Other ways to read this feed:
