The Web is 20 years old and its impact on journal reference management

I got this email from a certain Anderson Brown on the BioConductor mailing list. It actually lists some useful tools after a slightly wordy introduction and before a sales pitch (actually WizFolio offers a free account limited to 100MB or 200 items). Enjoy!

Hi,

March 2009 marks the 20th anniversary of the invention of the Web.   Like all great inventions, it arises out of an unmet need that badly needed a solution.  Tim Berners-Lee foresaw the great potential that can be unlocked by connecting data across disparate operating systems.  You can see the full talk by Tim Berners-Lee as he explains it at: http://www.ted.com/talks/tim_berners_lee_on_the_next_web.html

Fast forward to 2004 when the term “Web 2.0” was first coined.  This term now generally has the connotation of instant “read-write” and increased connectivity on the Web as exemplified by applications like Facebook, MySpace and Twitter. How will such technology impact upon the busy scientists’ workflow in terms of searching, compiling, organizing, sharing and analyzing peer reviewed journal articles?  A new crop of journal reference management applications have emerged within the last 18 months.  The term “journal reference management” is used here as opposed to the older term “bibliographic management” to emphasize the importance of managing and linking the bibliographic data with the PDFs.

The biggest frustration for the busy scientists is the difficulty of locating and managing the PDFs from a set of bibliographic data.  I have listed a number of recently released journal reference management applications that addresses to a certain degree this frustration.

Zotero – A research tool that helps you gather, organize, and analyze sources. www.zotero.org

Labmeeting – Organize, search, and store your paper collection and lab protocols. www.labmeeting.com

Pubget – Similar to Pubmed, except you get the PDFs right away. www.pubget.com

Mendeley – Academic software for managing & sharing your research papers. www.mendeley.com

At WizFolio, we started 2 years ago with a vision of creating a web based application that would manage bibliographic data and PDFs with the same ease that you would MP3 files.  Tightly coupled with the application is a citation tool that the user can customize on-the-fly with instantaneous preview.  We invite you to give WizFolio Web 2.0 a try at www.wizfolio.com and appreciate any feedback and comments that will make the application better.

JabRef – a free and powerful citation manager

JabRef is clean and powerful bibtex manager that works well with LaTeX writing. There are even some guide on how to use it with Word 2003 or Word 2007 and dedicated softwares for Windows.

One of the best features is that it can do a fetch Medline (function F5) when connected to the internet. You just need to enter the PubMed ID and it automagically extracts and stores the data in the bibtex format. All you have to do then is to give it a key.

And best of all, it is free as in beer (i.e. zero cost) and free as in speech (i.e. open source).

Review of IBM Lenovo X41 tablet PC

I been using my tablet PC laptop – IBM Lenovo X41 – for a couple of months now and though I should write a review on it. I believe the X61 sports a similar design except with a faster dual core processor.

PROS:

• Weighing around 1.6kg, it is classified as an ultraportable and it certainly feels that way.
• The ink and pen experience is fantastic. I am not too worried about scratching the screen now.
• Good build design and solid feel. The swivel hinge is solid even when using it on a moving vehicle. The extra girth is good for gripping in tablet mode.
• Full sized keyboard and very responsive.
• Built-in utilities software for backing up, restoring etc. I haven’t used it much but many do compliment IBM on this.
• (minor) Does not run too hot which is nice especially when using it in tablet mode.
• (minor) The microphone is of a decent quality and works well (except in tablet mode where the lid covers the mic)

CONS:

• No mousepad! Why? Can anyone explain to me why IBM / Lenovo abandoned the track pad in favour of only the track point (aka the “nipple”), and thus alienating a large number of laptop users?
• When the laptop is under heavy use, the cursor randomly jumps about.
• The speakers are placed at the bottom of the laptop. Solution: place the laptop on top of a book or something hard, so that the sound is projected better.
• No integrated webcam. OK, I can understand my refurbished X41 was released in 2005 when integrated webcam were not standard. However, Lenovo could have upgraded this feature in the X61 which was released in 2007.
• No in-built optical CD or DVD drive. Not a big deal if you are willing to work from the USB or network drives.
• Hard disk clicking problem – this is a well known issue with the X series.
• (minor) The keyboard layout is such that the bottom left most key is function (FN) key instead of Control (CTRL) key and there is no Windows key. Solution: There are softwares to remap the keyboard.

Verdict: If Lenovo integrates a track pad (with or without the track point), a webcam, improves the keyboard layout deficiences and perhaps an integrated DVD burner in the next version of their tablet PC, then I will be placing an order when it comes out.

Laptop stands

Ever since I saw my friend’s laptop stand (Ergo-Q by Bakker Elkhuizen), I have become convinced that one is needed to alleviate my neck and shoulder ache problems, which is probably due to me constantly hunching over the laptop.

Problem is that there are simply too many options available. So I decided to list down the features I needed in order of importance:

1. Usability – should raise laptop to at least my eye height
2. Portable – light weight and slim to fit in my laptop bag
3. Design – material that helps my laptop to cool faster
4. Stability – must withstand my occasional bumps and accidents
5. Price

I was lucky to come across Laptop Stands UK website which displays the pictures, specification and price of many laptop stand products (but strangely not those by Bakker Elkhuizen). Along with this website and googling, I narrowed down to the following models that met my criteria

• Ergo-Q by Bakker Elkhuizen

• Logitech Alto has a very nice integrated keyboard, stand and USB hub. There is also no indication as to the maximum tilting angle for the laptop stand and if it will allow variable height settings. The combined keyboard and stand appears to be useful but I am not sure if the laptop would wobble as I type on the keyboard due to the integrated nature of this product.

• The LaptopEasel which is nice but not exactly portable

• The Cool Laptop Stand which I later discarded as I was unsure if it allowed me to vary the height of the laptop and I was not sure on the stability issue. Plus it looked like something I could build myself.

• U Top which is the cheapest of the aluminium fold-away stands

• Lapjack which has a nice integrated document holder
  

• Ergofold

For the more adventures DIY person, you might want to try building your own laptop stand but perhaps with different material that might better conduct heat.

PS: I ended buying the Ergo-Q for about half the retail price from ebay. I been using it for the last 6 months (yes, this this post was drafted more than 6 months ago) and extremely happy with it as it has significantly reduced my neck, shoulder and back pains from using the laptop. I would happily recommend this product to anyone without hesitation.

Proof that (some) geeks are dedicated fans of Star Wars!

Normally I do not bother with any kind of fan tribute and least of all fan tributes for Star Wars that I am not personally crazy about (no arguments here please!). But I felt that this wonderful website deserves a special mention in recognition of the efforts put in. This site replays the entire original Star Wars film in ASCII (that is plain text folks)! It is absolutely bloody marvellous and IMHO more interesting than the real one.

I vote the next Star Wars film (7th or 0th or any other number George Lucas thinks will make more money) should simply be made in ASCII.

If y0u want to impress your friends even more, then simply telnet towel.blinkenlights.nl

LaTeX center aligning paragraph columns in tabular environment

I frequently use the table and tabular environments in LaTeX. And I use the paragraph column very frequently as it allows me to control the required width. The one drawback to using the paragraph column is that it is left-aligned and I often need it to be center-aligned. This has been driving me potty. Finally after about half an hour of searching today, I managed to stumble across the solution! Hallelujah

Marvel at the simplicity of this hack here. I love LaTeX and and the fantastic community around it.

Web 2.0 … The Machine is Us/ing Us

Ever wondered what Web 2.0 is or what is all the buzz behind it ? Then watch this catchy clip on the evolution of the web and what the future holds.

And one IM software to rule them all

Like many people, I manage multiple Instant Messengers. To be precise I have 4 that I can recall so far: ICQ (I think I had this since 1997 – almost a decade now!), MSN, Google Talk and Skype.

I like to bring people’s attention to one wonderful software called GAIM that is able to manage many different types of Instant Messengers. So far I managed to support ICQ, MSN and Google Talk. I have not figured out how to use Skype on GAIM yet. If anyone has any idea, please let me know.

There are other advantages as well. First, it is completely free for use. Second, it runs on multiple platforms. I have run GAIM on Windows, Linux and Sun Solaris without any problems. Finally it has a simple look and feel but this may be an advantage or disadvantage depending on individual taste. Perhaps using different themes is an option for those who find the look too simplistic.

Please note that I have not tested or even checked the existence of voice and video chat functionality as I hardly ever use them.

Sun’s Project Blackbox

I want one of these for my next birthday!

Here are some sample scenarios of where the blackbox could be deployed.