Monthly Archives: September 2006

Moving ELNs offsite

I have been experimenting with several web based organization tools mostly to keep my research activities running smoothly. The service I use most often is Backpackit. On Backpackit, I have a separate page for each of my research projects. Ever project page has a series of notes describing daily experiments and all associated files and documents are neatly organized at the bottom.

I also share these pages with collaborators and research technicians. All of who periodically update and annotate the content and rely on it to keep their own information in-sync. The ultimate aim apart from using them an organizational tool is to publish all of this. In Backpackit, these pages which are presently shared by only a few researchers can be made fully public and viewable to one and all. At that point I am sure they will be indexed by search engines and thus my data will be freed from the confines of my paper and binder lab notebook.

The service costs $5 and also guarantees me absolute peace of mind. Having had three machine crashes the last few months I never once winced knowing that my notebook and its contents are safe at Backpackit. Another big plus is that I have access to it from every OS I use using a very nice firefox plugin .

All of this brings me to an article I read about the end of venture capital . The article talks about an IT company not very different from the lab I work in. Its a small company run by a dozen odd people which used off-site services to streamline and “virtualize” its operations. Consequently they had yahoo handle their email and site hosting and Jotspot handle their backoffice for just $15 a month( talk about value for a small business). All of this left the company with time and resources to concentrate on their main product. Importantly they did it all without spending a dollar in venture capital.

Now replace the company with any typical NIH funded lab and replace venture capital with university overhead or NIH funds themselves and I really think the article has a lesson for any research lab. Just like outsourcing sequencing reactions or antibody making services, I think there is tremendous value in moving lab data archival and indexing off-site leaving me to concentrate on the research.

Having all my electronic data off-site does tie me down to the network but soon I have to worry a lot less about backups or viruses in my campus network. Added to all that , if I use a service like backpackit I can make all lab-bench data public when I publish a paper with the push of a button.
Now there is something to be said for that and moving ELNs off-site.

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* The Business|Bytes|Genes|Molecules has a post on SAAS and utility computing. I could not agree more : there is tremendous value in virtualizing for everone ranging from small biotech to an even smaller me everyday average Joe researcher and its amazing how much all of this truly moves us closer to the SUN adage the network is the computer or an even more cliched one “The Browser is the OS”

* John Udell a has a nice screencast about jotspot here


Great software

Warning non omics tangent ahead.

Its been a whole two months since my last post. In the last few months I have had a unix laptop hard-drive crash and its reiserfs file system irrecoverably “trample on itself ” , a windows XP installation get corrupted and loose all video performance after a system update, and both of this resulted in my buying myself a macbook pro running OSX .
These experiences made me ask myself that while I struggle with understanding protein structure and function correlations in my professional life, why cant engineers and scientists who deal with the vastly more predictable world of technology, build machines or systems that just do the right thing ( alright I use this apple add-speak because I just love OSX so far).
I then paused to ask myself , which are the recent technologies that have made my life so incredibly easy that they probably did represent significant achievements in software design or were probably the cumlination of people who wrote software that “did the right thing”. Using as a criteria , software or systems that I use so extensively and thoroughly that they are as much a part of me as my arms and legs , I made myself a quick “inapiration list ” in no particular order. They are Google , firefox , Microsoft Excel , a MySQl relational database , my home box running gentoo linux , the scripting language PERL and although still very new my OSX running macbook pro. I would also add the eclipse IDE to this list but that hope to be the subject of another post.

And as I was checking my gmail , in came an article on the SUN developer connection mentioning the 12 greatest pieces of software ever written. The list I was very happy to note included, every item in the above list I compiled in some way shape or form.
Google ( pagerank , no 11) , firefox ( well NCSA mosaic made no 6) , Excel ( no 9) , MySQL ( relational database no 2 ) , PERL ( the genome assembler coded in perl no 3) , and OSX ( based on BSD unix no 1 ) , gentoo linux ( also no 1).
I guess I am smiling because atleast I know a good thing when I see it. Charles Babcock I couldnt agree more.

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Web seminars – Science magazine . Flash goodness

For anyone interested in a great way to know about a paper and understand it ” in the words of the author” please check out the Web seminars at the science magazine site.

These are all very well done and almost a better medium than podcasts and plain audio or even full video to explain science results. They are as good an experience as sitting in a seminar room listening to the author talk with the advantage that you control the presentation and can loop back and rewind etc.

Created on the macromedia flash platform . It will be great to have one of these linked to every paper in every journal considering that flash is getting to be a great standard to base multimedia applications on.

Along these lines I came across an impressively intuitive AJAX based on-line presentation suite. Its called empressr and with a simple login you can create rich content presentations. I did a quick five slide quick presentation and the user interface was very easy to figure out.

It will be real interesting to see tools such as these used for putting more and more scientific presentations on-line in this day and age of shrinking print papers and expanding on-line supplementary materials.