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Todd Harris › Comments
Tenurometer: Add-on and Web Service for Academic Impact Analysis - http://tenurometer.indiana.edu/
suze, OpenSci Info, aarontay and 5 other people liked this
"Tenurometer is a social tool to facilitate citation analysis and help evaluate the impact of an author’s publications." A firefox add-on which works with Google Scholar. Looks interesting.
- Mr. Gunn
from Bookmarklet
Oof. Unfortunate name. Guess there is no reason to measure impact of those already tenured ;)
- Todd Harris
Looks to be limited to citation analysis as well which is a little unfortunate. Would like it more if they were explicitly collecting other social data around the papers and the users.
- Cameron Neylon
Tried it. Not bad. Publish or perish http://www.harzing.com/pop.htm returns more data, but is standalone.
- Björn Brembs
Can someone explain me how to use the plugin? I installed it, but see no menu, icon, or whatever show up...
- Egon Willighagen
In firefox, go to View/Sidebar - cute tool
- Rajarshi Guha
Ah, there it is... not sure how I missed that... thanx!
- Egon Willighagen
Playing around in #Balsamiq. Impressive while friendly at the same time. TIme to wireframe some #googlewave tools methinks
Todd Harris and Dan Hagon liked this
Great tool. And it's constantly evolving with weekly updates.
- Todd Harris
Apparently some issues with linux version so I think I'll play with the free web version (irritating popup every five minutes) until I get my Mac back and make a decision about purchasing...
- Cameron Neylon
An introduction to scripting in Ruby for biologists. - http://www.citeulike.org/user...
Todd Harris liked this
I like this as much as a Perl scripter can. ;)
- Todd Harris
Funnily that's exactly how I feel !
- Ian Simpson
from twhirl
Using BitTorrent to Retrieve Objects Stored in Amazon S3 - http://docs.amazonwebservices.com/AmazonS...
Todd Harris and Slade Publishing liked this
"Any object in Amazon S3 that can be read anonymously can also be downloaded via BitTorrent. Simply add a "?torrent" query string parameter at the end of the REST GET request for the object."
- Mike Chelen
Is that a security risk or a feature? :)
- Owen Greaves
Since the files are already public, it should be expected that people would download them. S3 bandwidth isn't free, so letting others help with distribution seems in the interest of the content author :)
- Mike Chelen
with a little more info about how the .torrent information is generated, could make a fantastic basis for file distribution
- Mike Chelen
This is a great feature of S3. Perl gurus might also want to see: http://search.cpan.org/~qantin... or http://code.google.com/p...
- Todd Harris
Byte Size Biology » A bioinformatician’s peeves (some of them) - http://bytesizebio.net/index...
Andrew Perry, Mickey Kosloff, Khader Shameer and 9 other people liked this
Could you have picked a more fitting picture with which to conclude that post? I laughed so hard. What's the source of that?
- Chris Lasher
Nice post, also applies to wet science- must contact all those collaborators and tell them what happened to th samples they sent...
- Richard Badge
from Nambu
@Chris it's one of those meme-ish pics that are everywhere. Don't know the source.
- Iddo Friedberg
from Android
Hilarious - perfect for hitting the trenches on a Monday morning. I'm always trying to instill in wet lab scientists that bioinformatics approaches are experiments just like any other and should be documented as such. Actually, I think bioinformaticists are often just as cavalier rarely taking good notes of their workflow.
- Todd Harris
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
- TRsdr
I'm on (thanks to Steve Koch!): tom.tullius@googlewave.com
- Tom Tullius
Plotzie, My Google Wave Robot - http://lee-phillips.org/wave...
Chris Miller, Claudia Koltzenburg, Peter Miller and 4 other people liked this
A google wave robot that takes lists of numbers and converts them to sparklines. Interesting because it does image insertion and other things but also because of the sparkline webservice it uses and the way it gets around appengine limitations
- Cameron Neylon
Good stuff. After looking at Cameron's ChemSpidey, Igor, and now this, I'm really getting excited about the potential for bots and in-line modification of the info-stream.
- Todd Harris
The (im)permanance of online biological resources - http://toddharris.net/blog...
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
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
Taking the morning off from polishing the manuscript to learn how to weld.
'Mummi' Thorisson liked this
Weld? wathehell. What do you need welding for, mate - to repair some farming equipment you tow around with a massive tractor, on a 1000-acre Montana ranch or wherever? :)
- 'Mummi' Thorisson
Welding is one of the best skills a bioinformaticist can have. The world will always need welders ;) That said, I'm pretty bad at it.
- Todd Harris
Bio-Linux 5.0 — NERC Environmental Bioinformatics Centre - http://nebc.nox.ac.uk/tools...
Danli, Cass Johnston, Endre Sebestyen and 18 other people liked this
"A dedicated bioinformatics workstation - install it or run it live. Bio-Linux provides more than 500 bioinformatics programs on an Ubuntu Linux base."
- Mike Chelen
from Bookmarklet
Neat idea- but how much of the 4gb USB stick remains for holding data / analyses: need a bigger stick?
- Richard Badge
from Nambu
This was one of the first (and probably best) of these distributions (think there was a BioKnoppix at one time?) It's been around at least 6 years. But a software suite is only half the battle. The biologist needs to know how to use the packages, store and interpret the output. Which is why we have bioinformaticians and IT staff. I've never been convinced that "bioinformatics on a stick" is much use to biologists compared with expert advice/support, but I may be wrong.
- Neil Saunders
Are these targeted towards biologists, or informaticians? Don't see biologists getting much use from such a distro, but do see computational types making good use
- Deepak Singh
Target market is what has always confused me. I'd assume that bioinformaticians are happy to install their own software locally and for biologists with limited tech skills, a live CD doesn't help much. But I'm happy to be proven wrong by success stories.
- Neil Saunders
I gave it to one of my students - we'll see what he has to say.
- Björn Brembs
Neil: making the software easier can help decreasing repetitive tasks, allowing more efficient use of expert advice and support, which is definitely the most valuable and scarcest resource. newcomers can often manage to boot the OS and start playing with some software, and experienced users can check if their software of choice is included, and save a little time when setting up new machines
- Mike Chelen
Deepak: looking at the package list http://nebc.nox.ac.uk/tools... some favorites of both fields stand out, for example a biologist may run a BLAST search regarding a DNA sequence they are studying, while an bioinformatist could develop applications with Bio-Java and Eclipse IDE
- Mike Chelen
Richard: data could be stored on a network drive, or a larger flash disk could be used, since there are 8, 16, and 32gb USB sticks available now pretty inexpensively. also, additional USB drives can be plugged in limited only by the number of USB ports on the machine
- Mike Chelen
Björn: cool, would love to hear how useful others find it. the software packages can also be installed in current Ubuntu systems by adding their repository http://nebc.nox.ac.uk/tools...
- Mike Chelen
Follow on question? Would a VM be equally useful? For example, I use VMs a lot to learn stuff and configure environments.
- Deepak Singh
Deepak: yes absolutely! for exactly the reasons you mention, experimentation and reliability. found a VirtualBox VDI image: http://friendfeed.com/bioinf... any more formats such as VMware or EC2 AMI would be great too :)
- Mike Chelen
there's a bunch of good EC2 AMI's that I will be highlighting either here or somewhere else soon (from familiar names), but more the merrier
- Deepak Singh
from IM
@bjorn please do get your student to feed back to NEBC, a long time ago Bio-Linux was my baby and my full time job. It's come a long way since I left it and I'm very happy to see that it's still going. It has its rough edges, and things which could be done better, but out of the box it's a well set up system ready to go. It's already been used as the base for other more focused...
more...
- Daniel Swan
@Neil with Bio-Linux I can happily say that we turned a few biologists into informaticians, and one into a programmer when I was with the team! Even last week a biologist walked into my office, asked me to help it getting up and running in VM on his laptop so that he could do some work. The Live-CD version was really just a distrubution method, we used to send out a bootable cd-rom that would netinstall a Linux image from our servers. Inefficient at best :)
- Daniel Swan
Good to hear. I remember when NEBC were setting up many years ago, Dawn contacted me regarding compilation of Phred/Phrap under Cygwin after I mentioned it on Nodalpoint. The early days of the bioinformatics social network!
- Neil Saunders
Deepak: thinking about combining the Bio-Linux packages with some of the standard Ubuntu EC2 AMIs from http://alestic.com/ since they are optimized already, and contain other common tools
- Mike Chelen
Mike, that would be brilliant. Lots of our customers ask for starting points in this space and being able to point to something that they might be familiar with would be great. Let me know when you do that. I am thinking about writing up a post on all the available bioinformatics AMI's on AWS
- Deepak Singh
Mike - you might want to talk to Tony Travis about this (ajt@rri.sari.ac.uk) he has interests in taking the Bio-Linux base in a more 'cloudy' direction, and I'm sure Dawn and Bela and co. at NEBC would be happy with any feedback along those lines.
- Daniel Swan
Deepak, getting the bio-linux packages installed can be done with a bash script http://github.com/mchelen... and maybe used with runurl http://alestic.com/2009... or to generate an AMI
- Mike Chelen
Daniel, almost all the packages install okay, are there any particular applications that would be important to test? here is how the desktop looks on ec2: http://ff.im/8fb8j
- Mike Chelen
Great idea. Anything to reduce the tedium of wget; ./configure; make; make install is welcome and helps lower the entry barrier for people into the field.
- Todd Harris
Todd: it would be nice to start an instance with the least manual input, especially when running a particular application. for example software set up to use a biology AWS dataset http://developer.amazonwebserv...
- Mike Chelen
<-- pure biologist, willing to install on top of current Ubuntu to give it a try. Agree with Todd on extra installs. I essentially only use a java-based app to chomp on big files, also Bioconductor on rare occasion. Neil's point about need for expert advice is well-taken, but I find that a biologist, willing to use a linux platform, right away gets more targeted feedback when asking for help.
- Heather
Heather: that's great, did you find it easy enough to add the repository? here's a script that can save a little time, it is only a few lines though: http://github.com/mchelen...
- Mike Chelen
The ideal way to install the repository would probably be a .deb containing the apt sources and signing key. This is used for example with Ubuntu One https://one.ubuntu.com/support... and PlayDeb http://www.playdeb.net/updates... (expand the instructions). Maybe someone could prepare this given the existing NERC repository info?
- Mike Chelen
Deepak: the Bio-Linux image from JCVI http://www.jcvi.org/cms... really looks great, anything that helps this project can benefit other researchers interested in running bioinf software on EC2. maybe a repository mirror within EC2/AWS cloud, or a public AMI, would help too?
- Mike Chelen
Mike that is a public AMI, ami id is ami-6953b200
- Deepak Singh
from IM
Deepak: found the wiki page now http://sourceforge.net/apps... thanks!
- Mike Chelen
anytime
- Deepak Singh
from IM
does this image include a desktop environment? the screenshot sort of looks like remote x. in most cases that is probably best, it could be nice to have a desktop version as well. thinking about slower internet connections, where some compression (such as freenx) is usually needed for remote desktop
- Mike Chelen
Not sure, you'll have to ask Bioinfo ... My guess is no, since I think it's built on a server image, but I could be wrong
- Deepak Singh
from IM
Deepak: that's good, been trying to find a way to get the bio-linux packages installed on 64bit instance. desktop could be handy for learning and testing
- Mike Chelen
I am my own model organism: getting genotyped (Part I) - http://toddharris.net/blog...
Bill Hooker, Nakao M., Adam Kraut and 10 other people liked this
Cool - I used to read sequence on films as well :-) Genotyping will be on top of my wish list for Christmas. I need to decide on 23andme , DecodeMe or another supplier. I may go with DecodeMe just to support them....if they still exist...
- Nils Reinton
@Nils: I'll detail why I went (initially) with 23andMe in a follow up post. But cost, data availability, and data sharing options where the main reasons. Navigenics charges $199 after the first year for updated analyses. And like you, I just wasn't sure about Decode being around for the long haul...
- Todd Harris
Hmmm. Having myself genotyped vs having a lasik surgery to get rid of glasses. On a student budget, can't really afford either, but the latter would be more bang for the buck. Would be cool though. But not via the service my ex-employers back home in Iceland offer - financial situation pretty dire currently.
- 'Mummi' Thorisson
Think I will put genotyping on my xmas wishlist as well. @Nils, @Todd: I too have read sequence on film; we are really dating ourselves by admitting to this!
- Bill Hooker
It's going to be the nerdiest xmas ever! One of my most exciting moments at the bench was reading off a sequencing gel late in the night, finally coming across the first mutation in a gene I had been positionally cloning for years. It was at the limits of resolution but still clear enough to poke your eye out. Seems mundane now, huh? I still think the readouts from old school sequencing gels are amazing - such a tangible way of seeing the unseeable.
- Todd Harris
I wish I'd kept a few of my old gel films -- I'd like to frame one to hang on a wall at home. Nerd art!
- Bill Hooker
Me too! I had a boxes and boxes of autorads, lost somewhere along the way during the inevitable academic life-shuffle.
- Todd Harris
@Bill, @Todd I'll dig out some of my old ones and send them to you for christmas...if you're lucky you'll get some of those with smiley bands in the corners and edges of the gel :-)
- Nils Reinton
I have one Google Wave invitation left. First come first serve.
Kubke and Jason Winget liked this
Please? toddwharris@gmail.com
- Todd Harris
meeee!!!
- Alejandro Montenegro
Sent. They said it will take a while until the accounts are actually sent out.
- Björn Brembs
curses! I woke up late today :(
- Jason Winget
i can't hardly wait to try google wave my email deva.born@gmail.com
- dev
The first of my invites have been sent out, I heard.
- Björn Brembs
The Protein Box Bot code for autoupdates of the Gene Wiki can be found at: http://code.google.com/p...
Nakao M., Mike Chelen, Andrew Su and 2 other people liked this
I love the "PBB" stuff we posted at Google Code, but it's admittedly a bit stale (in the services that it consumes and in the format it outputs). The new tool we have is at http://biogps.gnf.org/GeneWik... (for example, for PRKACB: http://bit.ly/332ed3). Right now this tool is only used for manual updates/additions, but it exports XML so we're planning on wrapping it in a script for mass updates as well...
- Andrew Su
Andrew, is the BioGPS code available? I was looking into PBB to extend what you've done but for genes from model organisms. There is a wealth of highly curated information I want to seed (and have the bot maintain).
- Todd Harris
Todd, don't know how I let this one slip by, sorry for the delayed response. You're interested in BioGPS code or PBB code? Both are possible, but both have challenges. Would love to think about working together if you've got something in mind...
- Andrew Su
ahh, now I get it, our BioGPS plugin for creating Gene Wiki content. yup, definitely possible. But you should know that due to WP's infamous "notability" guideline it can be hard to get model organism info put in en masse, but it's worth giving it a shot...
- Andrew Su
Google Sidewiki for easy annotation of scientific resources? http://toddharris.net/blog...
'Mummi' Thorisson, Mike Chelen, Cesar Sanchez and 2 other people liked this
Why they persist in using such a people-unfriendly term as wiki for annotations, I don't understand, though.
- Mr. Gunn
Good point. I've never liked "wiki" -- it seems a bit too cutesy and doesn't immediately reflect it's purpose. But PostIt is already taken!
- Todd Harris
wiki usually refers to content that can be edited by many people, often with some revision history and discussion features
- Mike Chelen
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
story: 1. X.Y. invites me to connect on LinkedIn 2.my reply: where did we meet? 3. his reply: we didn't but we share a common ancestor in the last few centuries - based on 23AndMe results on Chromosome 1 - and are both mtDNA T1a, which may be where the connection comes from. 4. I'm rethinking my LinkedIn connection policies :) (What would you do?)
Eric Heupel, Duncan Hull, Michael Habib and 7 other people liked this
He is not a professional contact. http://www.geni.com is a better choice :-)
- Pierre Lindenbaum
In the future, our social networks will be prepopulated for us at birth, saving us immense amounts of time. ;)
- Todd Harris
Yes, and there will be a chart titled 'probability-of-death=f(year)':-)
- Pierre Lindenbaum
I'd imagine that most of us share a common ancestor in the last few centuries?
- Neil Saunders
@Neil: reminded me of a paper I saw a few years ago, saying that the most recent common ancestor (MRCA) of ALL of us lived just a few thousand years ago. Along with this cool result: "Moreover, among all individuals living more than just a few thousand years earlier than the MRCA, each present-day human has exactly the same set of genealogical ancestors" http://www.ncbi.nlm.nih.gov/pubmed...
- Steve Koch
end of story, beginning another: I accepted the invitation because the person in question is a programmer w/ a strong interest in genetics & would like to go back to college to study bioinformatics & we started to build a connection around bioinformatics
- Attila Csordas
Hey, the Ig Nobel Prize winners are in: http://improbable.com/ig...
Iddo Friedberg, Andrew Clegg, Yann Abraham and 5 other people liked this
In re: The Chemistry Prize: For goodness sake, why would you want to turn tequila into diamonds? That's devaluing it ;)
- Todd Harris
ROFL.... so true...
- Alejandro Montenegro
Congrats to Newcastle Uni :) Glad to be from a Uni where someone's won an IgNobel! Newcastle press release here: http://www.ncl.ac.uk/press...
- Allyson Lister
First publication based on a collaborative effort using FriendFeed/TLS: The Gene Wiki: community intelligence applied to human gene annotation -- Huss et al., Nucleic Acids Research - http://nar.oxfordjournals.org/cgi... (via http://friendfeed.com/yokofak...) - Congrats to all authors
Todd Harris, Pierre Lindenbaum, Neil Saunders and 3 other people liked this
This isn't the first publication of the Gene Wiki which was first described in PLoS Biol in 2008:
- Todd Harris
Why do so few scientists make significant contributions and so many are forgotten in the long run? Richard Hamming, ‘‘You and Your Research’’ - http://wuism.net/readord...
Anne Tuukkanen, Bill Anderson, novoseek and 6 other people liked this
Without reading TFA, I have an immediate reaction of: s/scientists/people/g; s/research/life/g. "Whatever you do will be insignificant, but it is very important that you do it." --Mahatma Gandhi
- Chris Lasher
+1 Chris.
- tim
If you go through this 'TFA', you'll see that Hamming is not contradicting your Gandhi.
- Salvatore Loguercio
@Salvatore Certainly--I plan to read the article this evening and I'm not discounting it's worth. I merely wanted to point out the universality of the experience of insignificance.
- Chris Lasher
:) I agree, experience of insignificance is crucial. Perhaps human creativity could just arise as a reaction to this vast emptiness.
- Salvatore Loguercio
Haven't read the full article yet-- I've got too many tweets to read already -- but this is also touched on in Kuhn's work.
- Todd Harris
Because they spend to much time online. Now back to work!
- Eric Jain
@Salvatore After reading this talk, it's exactly what I thought it would be. Hamming has no time for "insignificant research". Here's the 30 second summary: 1) do nothing but research--I mean nothing, even at the cost of personal relationships, 2) talk to peers who do nothing but research, 3) don't fight the system, 4) you're only really lucky if you're prepared to take advantage of a situation.
- Chris Lasher
Well, a day after reading it I realized that I am going to forget his most extreme conclusions, while keeping several funny/interesting points across the talk. Some of my favorites: the concept of 'sound absorbers' in meetings, and the name spelled with a lower case letter as a sign of true greatness.
- Salvatore Loguercio
"He who works with the door open gets all kinds of interruptions, but he also occasionally gets clues as to what the world is and what might be important." I wonder if FriendFeed qualifies as an open door :-)
- Eric Jain
@Eric You propose an interesting thought. FriendFeed has allowed me to know of a lot of research going on outside of my own, and I'm familiar with a lot of names I wouldn't otherwise be. On the other hand, a better metaphor might be to view FriendFeed as a virtual coffee room or water cooler.
- Chris Lasher
Several Apache restarts/shift-reloads later, kind of working again. There's something wrong with GBrowse2 + caching that i don't understand.
Are you using it in a persistent environment?
- Todd Harris
I'm afraid I don't know what that means. Could you elaborate?
- Neil Saunders
We are experiencing technical difficulties and are currently running off one server. We will be bringing additional capacity online shortly.
We experienced a catastrophic failure of some of our "big iron" last night. Some creative re-routing and a server in the wings were called for...
- Todd Harris
Biological Curator position at WormBase-Caltech
Biological Curator position is now available at WormBase-Caltech. Please contact Paul Sternberg for more information.
Paul's email: pws@caltech.edu
- Todd Harris
Two WB users independently requested a way to access a simple ortholog summary list. I pointed them to the gene info feature of geneorienteer.org and she agreed that was what she wanted. Perhaps we can make it easier for people to find that site or to integrate it into WormBase?
Since we already have pre-calculated ortholog assignments, perhaps it would be easiest to draw out this information and make it more obvious.
- Todd Harris
What would be the easiest way to identify all the genes absent from the Ahringer RNAi library in a 5-10 map unit region of LGX? We've identified a mutant on LGX that we did not pick up in a RNAi screen, suggesting that it might be a gene absent from the library (barring the caveats that a clone from the library might not have worked).
Hi Christian. I would do this by generating multiple lists and then cross-correlating them. First, start with a list of all genes in the region. Next, fetch all RNAi experiments in that region. Finally look for diffs between these two lists. You should be able to generate these lists from WormMart.
- Todd Harris
WormBase on FriendFeed and Twitter
Have a question about WormBase that you desperately need answered? Drop us a line in the WormBase Help Desk group on FriendFeed. Want to keep up on system status and new features? Follow us on Twitter. Or subscribe to one of our RSS feeds.
WormBase changes curation procedure
WormBase will ask authors to specify the types of data in their papers using a simple "author first-pass form" that will be e-mailed. Your timely participation in this effort will help prioritize your paper for curation.
WebGBrowse - a web server for GBrowse - http://bioinformatics.oxfordjournals.org/cgi...
Pawel Szczesny, Krishna Mohan, Peter Miller and 7 other people liked this
The Generic Genome Browser (GBrowse) is one of the most widely used tools for visualizing genomic features along a reference sequence. However, the installation and configuration of GBrowse is not trivial for biologists. We have developed a web server, WebGBrowse that allows users to upload genome annotation in the GFF3 format, configure the display of each genomic feature by simply using a web browser, and visualize the configured genomic features with the integrated GBrowse software.
- 'Mummi' Thorisson
I can't believe that Bioinformatics (or any journal) still accept "make software palatable to biologists" papers. If you want Gbrowse but find installation/configuration too difficult, talk to your IT department or friendly local bioinformatician. If you can't be bothered to do that, I doubt you can be bothered figuring out how to generate GFF3 for upload.
- Neil Saunders
Don't know about GBrowse, but it's not uncommon for such applications to be a pain to set up (poorly documented dependencies, platform issues etc). Then there is also the issue that setting up a public server isn't trivial -- if done properly (security and availability etc). And finally, not everyone has a helpful IT department :-)
- Eric Jain
Have to agree w/ Neil - if GBrowse is too much, GFF3 certainly will be as well. Also doesn't ENSEMBL provide these types of tools and configuration of tracks already?
- delagoya
Ensembl is not necessarily a good option if you want/need to run stuff locally: it's far, far bigger + more difficult to install than GBrowse (though haven't attempted an Ensembl install recently...).
- 'Mummi' Thorisson
I am with Neil (surprise surprise). Sometimes, even if you have good docs, complex systems are going to require expertise to install and maintain.
- Deepak Singh
Lowering the bar for using GBrowse, or any tool, is a good thing. You can argue that producing GFF3 is still too difficult, but it's a step in the right direction. I like seeing re-use and improvement projects getting recognition. I would rather be helping a biologist produce GFF3 so they can browse the data themselves than setting up and configuring servers. The more that can be automated and simplified, the more cycles we can spend on interesting new questions.
- Brad Chapman
I agree with Brad, but franky, I'm a bit mystified by this. GBrowse already has upload functionality. What most users want to do who have the wherewithal to upload their own data is see in the context of other data.
- Todd Harris
The manuscript could have been better. One of the strengths I noticed with WebGBrowse (which the authors failed to highlight) is their glyph library. The glyph documentation under bioperl is not exhaustive and with several errors. More over, it aims at perl programmers, not the users/biologists. I always wanted to know the complete list of parameters that go with each glyph and WebGBrowse has definitely answered this particular problem.
- Krishna Mohan
BioInformatics Web Developer - http://bioinformatics.ca/resourc...
'Mummi' Thorisson liked this
Feel free to contact me if you have questions: todd@wormbase.org.
- Todd Harris
are you at OICR now?
- Paulo Nuin
I met folks from wormbase just last month
- Deepak Singh
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