Cass Johnston › Likes

Ricardo Vidal
The more I use R, the less it seems I understand what's going on... #needMoarCoffeeee
Pierre Lindenbaum
I've uploaded my presentation about "Next Generation Sequencing" on slideshare:
I believe you missed the citation of this paper, and perhaps others, for the 454 figures - Chris Lasher
Jan Aerts
The unsuccessful self-treatment of a case of writer's block
Abhishek Tiwari
No, shut up. They just want a folder. A folder that syncs.
Jan Aerts
Getting Creative Things Done: How To Fit Hard Thinking Into a Busy Schedule
Awesome post! I'm working with some brand-new, never-been-academics clinical faculty members who must now publish and this sort of scheduling stuff is actually their biggest concern -- very timely! - Mickey Schafer
This seems key: "the inviolable nature of the scheduled creative blocks, combined with the strict rules for avoiding interruption during these blocks, enables a quick shift of mental mode." Obviously that works for the author; if it doesn't work for you, the whole system collapses. But I guess you have to give it a fair trial before you can know whether it will work for you. I think I might try this. - Bill Hooker
The group I sent this to liked it very much -- but they are an unusual gift for a teacher -- grown up professionals who understand that new work has a learning curve, and are willing to learn how to manage academic life with no ego getting in the way -- I plan on enjoying it while it lasts! Personally, I started using a system like this about two years ago -- not as disciplined as I should be, but I can anecdotally confirm that my productivity and stress control are both higher when I follow my routine. - Mickey Schafer
Chris Miller
"Perl – The only language that looks the same before and after RSA encryption." -- Keith Bostic
Unreadable? - Egon Willighagen
:p pff, I will not be forced to indent my code ! :) - Pedro Beltrao
And Perl is the only language that has both "white" and "black" magic. :) - Pawel Szczesny
Rutger Vos
A Visual Survey of Tree Visualization -
What no geophylogenies! Otherwise quite wonderful! - David Kidd
Andrew Clegg
Excellent. Actual vs Predicted Usefulness:
Andrew Clegg
#puppet -- a very satisfying way to spend a day automating what would have taken 5 minutes by hand
Mike Chelen
"Today marks reaching Drupal 7's 0 critical bug milestone! We've rolled one final beta release to shake out any last minute problems and fix strings. Please help! This release includes: Upgrade to jQuery 1.4.4 and jQuery UI 1.8.6 Numerous upgrade path fixes Numerous accessibility fixes All critical bugs fixed! For the full list of changes, see the release notes." - Mike Chelen from Bookmarklet
Jonathan Eisen
Awesomics: kind of a #badomics word but tongue in cheek and site is nice -
Rachel Lane
Infographic of the Day: Clock Knits Time Into a Scarf via @fastcodesign thought you might like this @whoopdedoo
Andrew Clegg
The iPhone suggest dictionary has 'Odontoceti' (toothed whales, a suborder of the Cetacea) but not 'shit'. Hmm.
Jan Aerts
RT @infosthetics: The End of Network Graph Hairballs: Linear Network Layouts
Got another request to use webapp from 2003 paper. I, er, don't have it any more. Where can you "freeze" webapps and host permanently?
I think standalone AMI's (a la galaxy) are always a good idea, and with micro instances might be even cheaper - Deepak Singh
Has anyone built an app/webapp archiving service? Something that makes it nice and easy to roll an AMI? Or is it so easy that anyone providing an app _should_ be able to do it? - Cameron Neylon from twhirl
If you have an existing app and it's got a fairly well defined environment should be relatively trivial with some docs. Launch AMI with the right security group, log into URL. - Deepak Singh
Or make the code available so that it can be re-instantiated. - Deepak Singh
I should have a go at it. I think I'm probably fairly typical of the "might write some code but not done it before so find it a bit scarey" type. I can see a case for a service but can't really see what the long term business model for preservation would be... - Cameron Neylon from twhirl
"...can't really see what the long term business model for preservation might be." That made me LOL. You aren't the only one ;-) - Mr. Gunn
Marius, that's my argument, especially in forms that don't need to be "hot", but provisioned as required. Alternatively, it is an interesting "library of the future" problem - Deepak Singh
Our webapps are not hosted on an old machine, they're hosted on a cluster with an infrastructure for queueing jobs from the webserver to compute nodes, updating the database (on another node) and the filesystem, etc. We have two full-time programmers working on them along with myself, plus we get sysadmin support from LBL. I don't think it would really be reasonable to ask the publisher to host that, they're not in the web application development business. - Ruchira S. Datta
I would like to roll AMIs some time, hopefully sooner rather than later, but I'm rather skeptical it's going to be "trivial". - Ruchira S. Datta
I once believed that virtualization could help solve the impermanence challenge of scientific resources but was ultimately stymied by all the problems pointed out by @Ruchira. Neil points out another inherent problem, that funding for specific projects is often connected to specific personnel and once they move on, the resource is sure to break with the next reboot and security update.... more... - Todd Harris
I'm glad people are warming to the idea of packaging up code+databases as a working VM to be included 'supplementary data'. I can remember suggesting something like this on Friendfeed a long while back and being somewhat shouted down .. which was probably fair in the case of apps like Ruchira's. But for single node apps with databases in the order of 10s of gigabytes, I think it's... more... - Andrew Perry
There are always apps that don't fit the bill (e.g. Porting Galaxy was non-trivial), but for many apps, it's not that hard. In the future, Todd's suggestion is the right one, in that we should think about it at the start of the project and it should be part of the process for larger projects (where there is significant investment into developing the app or service). I do think that... more... - Deepak Singh
Deepak Singh
Matt Wood
Deepak Singh
Platforms for data science -
Platforms for data science
With many thanks to @mza - Deepak Singh from iPhone
"data is a royal garden" : Like++ - Khader Shameer
Jan Aerts
ECCB10 talk - Next-generation sequencing and structural variation -
ECCB10 talk - Next-generation sequencing and structural variation
Jan Aerts
Michael E. Driscoll
my brain is a thin layer on top of Google.
so true... - Yann Abraham
Yann Abraham
Great, inspiring slidedeck: Check out this SlideShare presentation : What has the public ever done for us...?
Andrew Clegg
RT @bengoldacre: Epic column in the Irish Times: deserves a place in nerd history
Jan Aerts
This scares the hell out of me.
This scares the hell out of me.
What is it? - Egon Willighagen
"Now you can go crazy with BioInformatics" ?! - Cass Johnston
That's scary indeed... seems to depend on closed source platforms... but the graphics are cool, and that's what matters, right? - Egon Willighagen
Are we all scared of how poorly this is aligning or am I missing something? - Rutger Vos
what alignment? that's not supposed to be aligned yet, is it? No, I'm scared of more vendor-lock-in... MS plays the game brilliantly, though... hat off for that. - Egon Willighagen
I guess I did read the picture incorrectly. Sorry :) - Rutger Vos
Yes, that's what we need. More people using excel for bioinformatics *facepalm* - Chris Miller
FWIW, one of the pieces of code mentioned, NodeXL, is actually open source, though Excel-only. I'm not sure how they are using it in this demo though. - Mike Chelen
Kaitlin Thaney
this is absolutely brilliant, full of WIN. "four levels of social entrapment" by hyperbole and a half ( HT @louwoodley
Yeah, I've found the social expectations about monitoring and responding to be very different among ages, but particularly between American and UK groups. - Mr. Gunn
Shorter Neil: kthxbi: it's not just for text anymore. - Bill Hooker
Wow, Level 1 and 2 describe 90% of the conversations I've had in my life. - Benjamin Tseng
Ricardo Vidal
I can work on code for hours without falling asleep. I can fall asleep for hours without reading a page of this paper... #whatsWithThat
A very different level of engagement with the process and information transfer. - Cameron Neylon
Jonathan Eisen
Am looking for systems for my lab to make electronic lab notebooks - suggestions? wiki? OWW? software?
Jonathan - we're collaborating with the group at Southampton (see which is basically a blogging functionality but we are hoping to enhance it as we use it, e.g. to have better automatic interactions with department instruments. It was important for us to be able to be involved with a group that are actively changing their system in response to our needs. It was also crucial to be involved with an open platform. - Matthew Todd
I like WordPress blogs, versioned, subscribe to RSS feeds of your student's work, HUGE GPL community. - Dave Lunt
Depends a lot on what you want from it and what kind of work it is supporting. The Southampton systems are getting a lot better and possibly more importantly a lot easier to add functionality onto. For some types of science they are probably good enough - for others, as I guess Mat is finding with wanting to put chemical structures in a native way - its not quite there yet. I find it... more... - Cameron Neylon
Steve Koch's group are the masters with using OpenWetWare, wordpress could probably do a lot of what you want if you've gt people prepared to do a bit of php wrangling...I think the main thing is not to think "I want an ELN" but to think hard about what you want to capture, and how important it is to structure that. A group DropBox folder that people dump Word files into can work just fine if what you want is just a backup and notification mechanism. - Cameron Neylon
I've long wanted somebody to work with Peter Sefton to make ICE into an ELN ( - Bill Hooker
CAMERON - I want a system where people record EVERYTHING they are doing in their research with links to all data, analyses, output, etc. And I want access to it from anywhere. And I want to be able to search it intelligently. Dropbox won't cut it. - Jonathan Eisen
I built our lab site on drupal, and I have considered adding this sort of functionality into it. Development Seed's custom drupal distribution Openatrium ( looks pretty cool too as an "intranet in a box." I can see that being compatible with your concept. - Walton Jones
@Walton - interesting - Matthew Todd
Jon - OK, that's a big ask to make it work. Technically all this is do-able and it is exactly the concept we are working on. Capture everything, and make connections between things. So what is next on my list is trying to connect DropBox to our blog system. This would mean that dropping any file in gets uploaded - the idea being that a web service is watching the subscribed drop box and... more... - Cameron Neylon
We've been using Wikispaces as the lab notebook and Google Spreadsheets for numerical data for a few years and it meets our requirements. Both have version tracking and we have code that enables full archiving of the notebook and associated raw data files. They are free and hosted so nothing to install and maintain locally. Google Spreadsheets has a nice API for querying and visualization of data if used as a platform to organize data collected from multiple experiments. - Jean-Claude Bradley
@Frank that sounds good. Are there easy ways to link a normal CMS to GIT/SVN? They tend not to be very user friendly, bad interface, which reduces uptake of the whole system in my experience. GIT plugins maybe for WordPress/Plone/Drupal? - Dave Lunt
I don't think there is any Git plugin for Wordpress but if memory serves there are some Wiki frameworks built on a Git backend. I still think worrying about the back end is putting the cart before the horse. Your average lab would probably not benefit from using a versioning system unless they understand what they're for. If they do, then they can probably just use it at the command... more... - Cameron Neylon
An issue tracker such as Trac integrates well with revision control systems, and includes wiki functions. This provides mostly annotation and discussion for the repository, so contributors must still push changes to the code itself. - Mike Chelen
Wordpress is great for logging stuff, but it kinds fails at the intelligent search aspects, unless there's something I'm not aware of - Mr. Gunn
@MrGunn Good point, I agree. Still, it kind of just works as an ELN, and its easy to actually start with today. - Dave Lunt
My requirements for an ELN are: (1) Support separate projects. (2) Complete text search. (3) Version manage all content, (4) Everything can be linked and tagged, (6) Display syntax-highlighted code snippets (7) Display images, video, etc (8) Synchronize with my pdf bibliography of references (9) Embeddable intelligent spreadsheets, (10) Display rss feeds and provide an rss feed, (11)... more... - Carl Boettiger
I'm wondering how many people here are experimental (wet-lab) people, and how many are theoretical/computational/electronic people? A lot of the things I'm interested in are to do with capturing the messy process of what happens in an experimental lab so that it can be searched and shared. Is that what everyone else has in mind? - Matthew Todd
My problem is I do both and want one system Sent from my iPad - Jonathan Eisen from email
I've been working on this tool that seems to answer you need: Give it a try? - Joel
Neil, I think the main distinctions are that in the wetlab things aren't automatically captured in the same way that they all sit on a disk somewhere for computational work. One of the big problems I have is getting people to see the value in making a record of all the samples that they create. There are very few systems that make this easy and natural. And it seems to make no sense... more... - Cameron Neylon
Actually I'd also throw your comment back at you. Descriptions of computational _process_ would be a lot less problematic if computational scientists stopped thinking that just collecting all the outputs was job done and learnt how to keep a high quality wet lab style notebook :-) Versioning systems capture outputs but rarely is there a good record of what _happened_ beyond some sort of commit message or a log file. - Cameron Neylon
I agree with the sentiment but not the details. I think a versioning system is overkill and not really the right paradigm for the lab scientist in most cases. In my experience you generate the data once, and then it doesn't change much. You process it, generating new stuff, but the kind of cycling, tweaking, and branching that VS are built to support doesn't really apply as much. You... more... - Cameron Neylon
There are so many different kinds of data. One researcher might be managing thousands of microscope images every day, while in the same time another could record only a half dozen numerical results. Saving revisions of the images could be pointless if each is only written once and never modified. Whereas putting a document under revision control is a great way to ensure that nothing... more... - Mike Chelen
Ah ok. I think we have a philosophical difference here then. I don't see processing as versioning, for much of my work at least, because it usually generates new objects of new types. I do agree that where you are manipulating a single object in a repeated way, perhaps with branching, then versioning (and branching) is a good way to think about it but I'm less sure that it is a useful... more... - Cameron Neylon
...and I do think that versioning systems (including branch and merge) should be a basic feature of any file system. Just not sure that they need to be surfaced for most users in many use cases. - Cameron Neylon
I'd go further actually, generating, storing, analysing and publishing research objects, explicitly including samples and other physical objects. And I think the "computational thinking" approach might be even better applied to the physical world. - Cameron Neylon
Cameron I think that the requirements for version tracking may differ between labs. In my lab we often have lots of undergrads recording their lab notebooks and it would be unusual if there was no error correction for an experiment at some point. It is also not uncommon that the Google Spreadsheets we use to record the raw data and show the mathematical processing often initially... more... - Jean-Claude Bradley
If you want everything consistently done in git the documentation part could be handled with toto - "a git-powered, minimalist blog engine" ( (not sure if you need commenting functionality) - Konrad Förstner
We've been very happy with Unfuddle. It includes notebooks, though I don't know how appropriate these would be for experimental data. The integration of the subversion repository with tickets / milestones / projects is very nice. - Ruchira S. Datta
biological data, at the point of capture, is really messy, and you often have to iterate several fast optimization kinds of assays or experiments before you hit on the set of conditions under which you can capture clean or meaningful data. Then once you do get close to clean, it's off to the next set of optimizations for the next thing. That's the dynamic that computational tools fail... more... - Mr. Gunn
A bit late to the party (via Cameron's post on the Daily Scan), but back in February I was sat in a dull seminar and made these notes. A Data Analysis Deposition System e.g. to store all the R code used to turn data X + Y into results Z. - load source code for analysis pipeline - check data dependencies, on submission and periodically in future (e-mail owner if links go down.) -... more... - Dave
Open Source develops web and CMS based LIMS - used in chemistry, agriculture, water quality, environment and inter-laboratory sectors. A public health lab branch is currently in development. Your requirements are research orientated, batching per project and full text admin are gaps in Bika that can be plugged. Full Plone CMS functionality is available. Analysis work... more... - lemoene
I've been using git for curating my (text based) data analysis in the social sciences, and I've been impressed with its usefulness for keeping a very detailed history of what I've been doing. The only problem is for large binary objects, but apparently that's being addressed. Gitalist: is a front end to git which can be easily modified to provide... more... - k d
There has been some very interesting discussions here, and a lot of questions that are commonly asked. There appears to be a lot of discussion about using software that has not been specifically designed to be an ELN and some people find that these are perfect for what they need them to do. However, it is important to outline your requirements (as has been done above). I work for... more... - Aaron Norman
I'm developing a collaboration tool for researchers called SciTecMed [ ]. It is like a mashup of dropbox and github. I'd appreciate an opportunity to show the demo and learn more about your needs. - SciTecMed
hey scitecmed - drop me a line - am interested in this - Jonathan Eisen
I just discovered this interesting discussion. Two systems for electronic lab notebooks that I don't think have been mentioned so far are: eCAT, a commercial system from Axiope and Yogo / Neurosys . I haven't tried either myself as yet. - Mark Longair
Andrew Clegg
Writing/Coding: Clojure Series: Table of Contents -
A series on doing natural language tasks with clojure. I for one welcome our new functional overlord. - Andrew Clegg
Simon Cockell
Cytoscape Web: an interactive web-based network browser. -
Bioinformatics (Oxford, England) (23 July 2010) SUMMARY: Cytoscape Web is a web-based network visualization tool, modeled after Cytoscape, that is open source, interactive, customizable, and easily integrated into websites. Multiple file exchange formats can be used to load data into Cytoscape Web, including GraphML, XGMML and SIF. Availability and Implementation: Cytoscape Web is implemented in Flex/ActionScript with a JavaScript API and is freely available at CONTACT: SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Christian Lopes, Max Franz, Farzana Kazi, Sylva Donaldson, Quaid Morris, Gary Bader - Simon Cockell
Very neat! Well done! - Egon Willighagen
Other ways to read this feed:Feed readerFacebook