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Andreas Matern › Comments
A friend asked me this: How can I get my entire genome sequenced? Anyone knows if there's a company who can actually make that happen? (I know about 23andme & their SNP approach)
Ruchira S. Datta and Mike Chelen liked this
Illumina will do it, for about 20k: http://investor.illumina.com/phoenix...
- Chris Miller
thank you, Chris!
- Carlos Leiva Burotto
Define "entire"
- Eric Jain
from iPhone
I mean "entire" entire!! the whole genome
- Carlos Leiva Burotto
I thought that Complete Genomics were setting up to do this, at a cost that will trounce the competition, but don't know how far they have got...
- Richard Badge
from Nambu
@Carlos Leiva Burotto : I think you need to be more specific, how much coverage do you want? Complete Genomics can do this, but they are not offering their service to individuals, yet.
- Burak Kutlu
Even if you were able to go the complete genomics route, those ~35bp reads leave a large percentage of the genome uncovered, since you can't map reads that short to repetitive sequence. For that matter, even 75bp illumina reads leave some pretty large chunks. So "entire" is something of a misnomer :-)
- Chris Miller
@Burak Kutlu, my friend asked me this, because he just wanted to know if this service is currently available anywhere in the world.. It doesn't matter how much you have to pay, or if there is a little percentage of the genome that keeps uncovered. I found Knome service http://www.knome.com/home... , for US 68,500
- Carlos Leiva Burotto
Isn't Knome already sequencing Ozzy Osbourne's genome?
- Andreas Matern
Related reading: http://news.cnet.com/8301-27...
- MohanArun
CCL: How to perform an "Exact structure search" into eMolecules (or similar database) by using a large list of SMILES - http://ccl.net/cgi-bin...
Jean-Claude Bradley liked this
getting an error from that link
- Jean-Claude Bradley
Same here.
- Egon Willighagen
Same here regretfully, that sounds like a neat tool
- Andreas Matern
Here's the link: http://ccl.net/cgi-bin...
- Noel O'Boyle
that works
- Jean-Claude Bradley
I was a doubter, but mindmapping has helped with my current brainstorming problem. Liking http://www.mindmeister.com. Thanks @skoch3 !
Graham Steel, Steve Koch and Ruchira S. Datta liked this
Interesting, what surprised you about it? I have to admit to still not using it for anything serious...
- Cameron Neylon
I've been using FreeMind quite a bit - do you really like that online tool?
- Andreas Matern
I do like that online tool, though I've never used any others so I don't have comparison points....
- Heather Piwowar
Cameron, I was trying to flush out a problem that I didn't have any structured way to think about. Mindmapping let me give it enough nonlinear structure that I could ask myself "ok, if those 2 things are related, what else is like that" and then "well, what I'm trying to say is that those things there are actually related to this." A structure emerged. It may have happennded if I'd...
more...
- Heather Piwowar
people laugh but my advisor and I have cut apart pieces of paper and then shuffled them around on a table to figure out order and structure. sometimes old school still works :)
- Christina Pikas
Christina, I don't laugh -- I use that method a lot. Will definitely give mindmeister a look after Heather's comment "software didn't get in the way", which has been my beef with the few mindmap programs I've tried.
- Bill Hooker
I checked out freemind, xmind, and mindmeister. Xmind was the best software, but it didn't allow collaboration. Mindmeister was by far the best in terms of being able to work with another person and embed live-updated maps. But a bit clunkier than Xmind. I got a good vibe from the company, though, in terms of how quickly they answered my emails. My hunch was that they'd be around a while and keep improving their product.
- Steve Koch
Also I should point out that Mindmeister isn't really free. And also point out that Pawel pointed me to it a few weeks ago.
- Steve Koch
I can barely function without a mind map, so maybe shouldn't comment. No plan gets made, no article written, no artefact designed, no ToDo list made, without NovaMind! One key issue is "affordance": it has to be so easy and fall so naturally into your brain and fingers that it doesn't interrupt the thought processes. I tried Freemind but couldn't find that affordance point there...
- Chris Rusbridge
"Affordance" -- thanks Chris, now I know the word for the thing I want in software.
- Bill Hooker
Just got my Motorola Droid. What Apps do I need?
Try mytracks and pdanet.
- Demetri Mouratis
How do you like it? Why the droid and not the google nexus 1?
- Andreas Matern
Life before Google - http://thenextweb.com/shareab...
heh...
- Andreas Matern
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 Moss, 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
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
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
Hmmm... never realized that RDF also stands for "Reality Distortion Field" ala Steve Jobs-- no wonder so many folks have been such doubters!
Similar thing happened to me: Application Programming Interface they: Active Pharmaceutical Ingredient
- Andreas Matern
A lecture hall with ~100 PhD students: "Do you know what is an RSS feed ?" ... No... nobody knows.
sigh...
- Chris Miller
That actually makes me feel a bit better. When I talk to colleagues about APIs, WebServices, RSS, SOAP, etc. I generally get blank stares - or I'm told I speak like R2D2...
- Andreas Matern
At OCCBIO 2009 http://www.occbio.org/ "Applications and Analysis Strategies for Next Generation Sequencing" / Mark Adams CWU / Genetics slides will be on http://proteomics.case.edu
ROY liked this
uBlogging: General bioinformatics overview. Is starting with comparison of Solexa / SOLiD / 454 etc.
- Iddo Friedberg
> 100 x 10^9 bp / run in 1 year. Another interesting stat: 4x10^9: human dbEST: about the size on one Illumina run
- Iddo Friedberg
Big slide with lots of tools. All slides will be on http://proteomics.case.edu
- Iddo Friedberg
Commercial software. "Advantages": good graphics and run on PC. hehe.
- Iddo Friedberg
1 TB / image / run --> 80 GB sequence data
- Iddo Friedberg
MAP / Bowtie and ELAND (==illumina prop. software): all reads in RAM. Quality values are not taken into account?!
- Iddo Friedberg
35bp can be unique (20bp is enough for the human genome) : IF you are not in a repeat genome. It is possible to do 128x coverage of a bacterium using 0.25 of an Illumina run. But repeats may still hamper assembly, even if you have a reference genome.
- Iddo Friedberg
argh didn't see my hand. Wanted to ask about flow-space assembly
- Iddo Friedberg
basic overall intro to 2nd- generation assembly issues
- Iddo Friedberg
Great, looking forward to seeeing the slides!
- Andreas Matern
re: MAQ/Bowtie and ELAND, as far as I know, quality values are taken into account. Desperately trying to figure out how to use them for myself: http://ff.im/3SYRm but I am seriously lame.
- Heather
Nintendo ships over 15 million "Wii Fit" since launch - http://www.reuters.com/article...
and over 14.9 million are still unused
- Andreas Matern
Nintendo ships over 15 million "Wii Fit" since launch - http://www.reuters.com/article...
and over 14.9 million are still unused
- Andreas Matern
» Getting Things Done with PersonalBrain - http://blog.thebrain.com/gtd/
This time I'm really going to do it :)
- Andreas Matern
» Getting Things Done with PersonalBrain - http://blog.thebrain.com/gtd/
This time I'm really going to do it :)
- Andreas Matern
NCBI Genome Workbench Home Page - http://www.ncbi.nlm.nih.gov/project...
Bill Hooker, Marcos de Carvalho, Berci Mesko, MD and 5 other people liked this
Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results. Genome Workbench is built on the NCBI C++ ToolKit and uses cross-platform APIs for graphics. It runs on your local machine, and is available for Windows 2000/XP, Linux, MacOS X, and various flavors of Unix. Download recent versions from the NCBI Genome Workbench FTP Site , or choose one of the download links below:
- Pierre Lindenbaum
That's interesting, anyone using it yet with their own data?
- Andreas Matern
Genome Workbench Home Page - http://www.ncbi.nlm.nih.gov/project...
NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.
- Andreas Matern
Conferencing Services for Thomson Reuters - http://www.btconferencing.com/thomson...
8773840533
- Andreas Matern
Why 'Private Cloud' Computing Is Real -- And Worth Considering -- Cloud Computing - http://www.informationweek.com/news...
Companies that want the benefits of cloud computing services without the risks are looking to create cloud-like environments in their own data centers. To do it, they'll need to add a layer of new technologies--virtualization management, cloud APIs, self-service portals, chargeback systems, and more--to existing data center systems and processes. Be ready for a debate as you discuss this new way of doing things. Just the term "private cloud" irks some computer industry veterans, who argue that cloud computing by definition is something that happens outside of your data center, or that the technologies involved in private clouds have been around for years, or both. Even some of my InformationWeek colleagues pooh-pooh private clouds. "Nothing new under the sun," scoffed one editor.
- Andreas Matern
Senior Integration Engineer - Cloud Webservices at EMC Corporation (Cambridge, Massachusetts) - http://jobs.boston.xconomy.com/a...
Interesting job description.
- Andreas Matern
“Do BMC Bioinformatics readers understand UML diagrams? Internal estimate is that only 10% of the reader base would understand it... Is that a realistic estimate? How can we measure this? Has there been on survey on the informatics capabilities of BMC BioInfo readers?” - http://friendfeed.com/e...
Khader Shameer, Pierre Lindenbaum, Cameron Neylon and Rajarshi Guha liked this
Well I think we've established that I don't understand UML diagrams...
- Cameron Neylon
Can you show us the diagram? If it's just boxes with concepts and some arrows I think that's fine (maybe explain what the arrows mean). But if you're relying on the reader to understand the difference between composition and aggregation and instances vs classes that's probably too much. Unless of course this is just additional information that's not central to the understanding of the paper.
- Eric Jain
Eric +1. I'm able to understand a basic UML diagram , but I'm far from understanding the complete specification.
- Pierre Lindenbaum
And I would be curious to have this survey for some other technologies: RDF, WSDL,etc...
- Pierre Lindenbaum
Eric: first thing to realize that there are actually indeed several UML diagram types... what's the bare minimum of knowledge a bioinformatician should know? UML do not seem to be part of that... how specialized can a scientist be? The most common format for IT diagrams sounds like something basic... (and I don't mind s/UML/XXX/... someone who could read XXX, could read UML too)...
- Egon Willighagen
No matter how difficult the science is, a mere pointer to some paper is enough... a diagram in a not-so-complicated standard is a no-go... if I don't understand something, I make sure to learn it (as soon as I have time)... but seems to become rather uncommon...
- Egon Willighagen
Pierre, indeed!
- Egon Willighagen
There was a survey started by the ELIXIR project about this subject: http://www.surveymonkey.com/s... . It asks if the DB owners know about WS, if the results are downloadable , etc... but the results are still not available.
- Pierre Lindenbaum
I second Pierre. (Third?) I 'understand' UML diagrams, but the devil's in the details. I also would be curious to see a survey for other technologies.
- Andreas Matern
I dont read BMC Bioinformatics but understand the basics of UML. Ever so often while reading a paper that talks about some library or coding project, I wished the authors had provided a UML diagram to describe their design .
- Hari
user interface for the Blueprint CSS system
- Andreas Matern
from Bookmarklet
Searching for great examples of AJAX and bio/chem-informatics... Do people use AJAX for integration of data sources in the real world?
Khader Shameer liked this
Not quite sure I understand the question. Integration of data sources isn't exactly what comes to mind when thinking about AJAX
- Deepak Singh
http://www.ensembl.org is full of ajax stuff
- Pierre Lindenbaum
Sorry, I phrased that wrong. Do people have their favorite tools for data integration? Are there exemplary examples of AJAX bio-cheminformatics portals? The two questions are distinct, but my idea for an application would be a 'web2.0' portal page wherein one could query across multiple data sources...
- Andreas Matern
Thanks, Pierre. That xmap application is pretty interesting...
- Andreas Matern
Now that does make sense :). Also check out the Nextbio interface
- Deepak Singh
Thanks, the NextBio thing really does look interesting...
- Andreas Matern
http://www.jbrowse.org/test... (since apparently Ian is too modest...)
- Andrew Su
Note that browsers by default don't allow AJAX calls to sites other than the one that served the page, so all requests have to go through (or at least be proxied by) a central server.
- Eric Jain
Semantic Enrichment of the Scientific Literature 2009 (SESL 2009) -- end of the month at the EBI. Looks like the kind of thing some people here would be into - http://www.ebi.ac.uk/Rebholz...
Resharing from Andrew Clegg - this is a conference that I might have buck up and attend.
- Andreas Matern
Seventy Seven Shakes The Foundation at rileysmile - http://www.rileysmile.com/...
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Great new dance song!
- Andreas Matern
Seventy Seven Shakes The Foundation at rileysmile - http://www.rileysmile.com/...
Great dance mix
- Andreas Matern
Article Skimmer - http://prototype.nytimes.com/gst...
A great way to read the newspaper!
- Andreas Matern
For those not in school: if you could go back and study anything, what would it be?
timepilot, Mike Elliott, Ron and 23 other people liked this
Psychology or Archaeology
- pala
faceted search with Marti Hearst at UC SIMS
- Laura Norvig
Time travel. Why make it a hypothetical.
- DeWitt Clinton
Some more languages, specifically Arabic
- Shakeel Mahate
i often wonder and can't decide. possibly political science and international relations and/or economics. All as a second degree after my own, because I would choose physics again if it came to rewinding :). Linguistics and language processing might be another option. Oh I cant decide!
- Iphigenie
Anthropology
- Shevonne
Aviation
- Tracy Benham
Architecture
- Jake Sutton
Architecture
- Andrew Smith
Mathematics and economics
- Jaimini
Art and Design or Sociology
- Shey
Philosophy and psychology.
- Jen
Sociology. And probably econometrics. :-D
- Ordinarybug Heather
Philosophy, Psychology and fine arts (probably textiles).
- Lindsay
Languages. Maybe philosophy. Film.
- Jandy
Cooking
- peter
Astronomy
- Robert Cooper
from twhirl
Economics and/or partying
- Jim Norris
design
- Damien Franco
Macro-economics
- Bindu Reddy
I would KILL to be able to go to art school to study design and metalwork.
- Mark Novak
If I had the patients I would study something in the medical field!
- Brandy Lea
Computational Neuroscience. There's just more to learn there than I will ever be able to do in my spare time.
- Joel Webber
Textual Criticism.
- Joey Gibson
Anthropology, economics or fashion design.
- Jeanine W.
Anthropology and creative writing (im stuck on my book concept)
- InPerpetualMotion(Gina k)
Linguistic anthropology as it affects modern public policy, and also bike racing.
- Michelle Lee
Heh, I used to enjoy dismantling things. I could never manage to reassemble them though, sadly.
- Tyson Key
How to be a Social Media Expert! :D
- Josh Haley
music, graphics and psychology
- Vicky
English and journalism
- R. Ferguson
Architecture or Graphic / Multimedia Design
- JA Castillo
History, particularly 1900-1950
- Duncan Riley
Mathematics.
- Akiva
Business/marketing/finance (personal finance, that is). If I could (and I will never do it), I'd get my MBA.
- Tamar Weinberg
Business.
- James Ferguson
Child development/psychology. What I should have done in the first place along with getting my credential.
- Just Katie
Oceanography or astronomy. But happy with what I've done.
- Daniel Cornwall
Chicks and partying! Oh, wait, already did that. How bout metal shop?
- Hayes Haugen
Art and Math.
- Alan Le
Greentech wind turbine stuff
- adolfo foronda
Shenanigans
- Far
Early childhood education. I still might.
- Penguin
How to install cars in cars so I can ride when I ride. Actually I like what I studied very much.
- Josh Haley
Photography.
- Kol Tregaskes
@Josh - Hah
- Tyson Key
Probably glassblowing. There's something deeply satisfying about working with hot molten glass.
- Jeremy Brooks
Results Wordle here: http://www.wordle.net/gallery...
- Kevin Fox
Molecular Biology
- Jenny Morman
Wow - The Wordle is fascinating.
- Charlie Anzman
Meteorology
- MLx
Photography as well.
- David Cook
Art & Photography. I still have nightmares still being in school, so if I ever go back, it'll be for fun
- Rodfather
Architecture. Or photography. Or both.
- Kevin (barely visible)
I'm DOIN' IT! Studying massage therapy now. :-D Would still like to learn more photography, as well.
- Lisa L. Seifert | FHG™
Cognitive Neuroscience, maybe. I did think about it, but some interesting books, Kandel's _In Search of Memory_ and Marcus's _The Birth of the Mind_, convinced me that the road I took instead (Bioinformatics) is where it's at, at this point in time. I do hope to get back to Game Theory some day, and Artificial Intelligence was always appealing.
- Ruchira S. Datta
Robotics. Or cooking. Or brain surgery.
- Felicia Yue
Anything? Computer science .... or Creative Writing .... or Drama ... I'm so ... decisive.
- Andreas Matern
Music.
- Ron
autoCAD
- Faye
History and Literature
- Mike Elliott
Screenwriting
- Rachel Garb
Megan Hinton - artist - http://meganhinton.com/
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Boston artist, Megan Hinton, has a great sense of style and abstraction.
- Andreas Matern
This Is Absolution | DeathStarInc.com - http://www.deathstarinc.com/...
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Video of Killswitch Engage's This is Absolution
- Andreas Matern
Blueprint: A CSS Framework - http://digg.com/program...
"Yahoo does, but the blueprint framework is quite impressive. Looks good, easy to use, etc."
- Andreas Matern
Walking around Ia in Santorini... Stopped for yogurt with honey and walnuts-my favorite. Photos on flickr :-)
Wow, I really miss Santorini. Did you join the masses and photograph the Oia sunset? The view of the Aegean Sea and the sun is amazing.
- Michael Vorel
Wife and I honeymooned in Santorini, loved it there... very jealous
- Andreas Matern
Went there last july. Will never forget the view on the caldeira... Some photos: http://www.flickr.com/search...
- Guillaume Lemoine
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