Tuesday, March 9, 2010

10 Web tools, programs and applications that keep me sane



The very first thing I do every morning when I get to the lab is turn on my laptop (this is unless I did a bacterial transformation the day before, in which case the first thing I’ll do is check the incubator). Then, I usually review a number of things: I check my email, check the latest updates from my favorite journals/blogs, manage my PDF library, etc., in addition to organizing my lab day (although I usually do this the night before). To keep track of all this (which can be a lot) I use several tools and applications without which I would be a mess. Here’s a list of some of my favorites.

Let’s start with the Google stuff:

1) Gmail. OK, this is fairly obvious. I did try some alternatives, but let’s face it: Gmail rules.

I have customized my Gmail homepage though, using some gadgets from “Gmail Labs” (check for this logo () in you Gmail page):

a) Right-side chat: Moves the chat box to the right side of the inbox. This gives you some extra space on your left sidebar to put other things, for example:

b) Google Calendar gadget: Adds a box in the left column which shows your Google Calendar. See upcoming events, locations, and details (See image on the left and #4)

c) Google Docs gadget: Adds a box in the left column which displays your Google Docs. Shows recent docs, starred docs, and has fast search (See image on the left and #2).

d) You can add other stuff, by using “Add any gadget by URL”: adds a "Gadgets" tab to Settings, where you'll be able to specify the URL of any gadget. This gadget will show in a box in the left column. There are several third-party applications that you can add.

e) And finally, “Navbar drag and drop”: Allows you to reorder the items in your navbar using drag and drop.


2) Google Docs. As you can “create and edit web-based documents, spreadsheets, and presentations and store them online so that they can be accessed from any computer”, it is ideal for documents that are frequently used and updated by all lab members. Be sure to back-up frequently: you never know.

3) Google Reader. Fantastic web-based aggregator to keep track of all your favorite journals, blogs, news, etc. You can easily add subscriptions, email content to colleagues, add tags, share with friends, organize using folders, etc. You should definitely use this or some other sort of RSS aggregator/organizer (if you don’t even know what RSS is, see here).

4) Google Calendar. I use it to schedule meetings, appointments, etc. A great thing about Google calendar is its very customizable “Notification” system. You can ask for pop-ups, emails and even free SMS to be sent to you at any time you specify before a scheduled event.

Note that all of these fantastic tools and many other Google applications work on phones (and not only iPhones). Check Google Mobile for more info.

OK, enough with the Google stuff. What other tools and applications do I use?

5) Remember the Milk (RTM) A great customizable task manager (like a to-do list). Normally I’d simply use pencil and paper to organize my daily tasks (e.g. Neurospora transformation, colony PCR, etc), but this has worked great for me: no risk of losing the sheet of paper.

A cool thing about it is that you can add your list as a gadget to your Gmail homepage (see image on the right and #1d), so you can check and manage your tasks, email, calendar and access your shared docs all in the same place (your Gmail page). Some may argue that this is the same idea behind iGoogle, but the gadgets in iGoogle, particularly Gmail, are very limited. You can also access RTM through your phone and it's compatible with Google Calendar.

RTM is free, but you can pay for some additional functions.

6) Tweetdeck. I really like this (free) software for managing my Twitter account. It has a multiple columns format, an in-built URL shortener, and many cool features. Further, I like the interface. It’s also available for the iPhone.

7) Mendeley. Free reference management program. I only use it to manage my (huge) PDF library and access the articles quickly (like “Papers”, but for Windows PC). Its MS Word plugin for managing references in a document isn’t quite there yet: it still can’t manage journal abbreviations, so, for example, it won’t give you a bibliography in Nature’s format. For managing references in documents I use Endnote (and Endnote Web), although I may try CiteSmart soon: it seems simpler and quicker (both Endnote and CiteSmart are non-free).

Note, however, that the “Journal abbreviation” feature has already been suggested at Mendeley’s website.

8) Foxit Reader. A (free) small, fast and rich PDF reader (there's also a paid version with more functions).

9) Mozy. An online backup service. You can select what folders to back up (backup your lab folder!), and the software will do that on their servers automatically. If you have more than one computer and need backup and syncing, you may find DropBox more useful.
Free and paid plans.

10) Microsoft OneNote. For those ready to make the jump to a digital lab notebook, this is a very good choice. I must admit that there are several other alternatives out there that I haven't tried yet, but this works fine.

You may find many more useful tips, tools and applications over at ProfHacker (which you can also follow on twitter @ProfHacker), Lifehacker and Hackademe.

-
(Image sources: RTM Gmail Gadget, Calendar and Docs gadgets)


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Tuesday, March 2, 2010

A new way to fund Science: Search for Research



Fascinating. That's how I would describe the newest initiative at Benchfly, directed at raising funds for Scientists!


There's a video explaining everything (funny, check it out), but if you are super super busy, then here's a summary:

1) You download and install a browser toolbar from Benchfly (here)
2) Every time you use the toolbar, you help raise a little money which goes into a pot (courtesy of search engines, which benefit from the additional search traffic)
3) All the money raised is then doubled by Sigma, and the whole pot is given away to scientists!

But how? And to whom?

4) Benchfly will give away "Microgrants". If you are a scientist and would like a piece of that money to partly fund your research, you have to go to Benchfly's Facebook Page and describe you research in 100 words or less.

Who selects the winners? Notably, anyone with an internet connection. People vote at Benchfly's Facebook page based on the research descriptions provided.

The more toolbars downloaded, the more searches performed, the more money raised, the more microgrants can be awarded.

Get the toolbar and "search for research"!

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Sunday, January 17, 2010

BioKM Webinar



As my readers (and twitter followers) may remember, a few months ago I was a runner up in the BioKM Twitter challenge, which got me a one year account at BioKM and a great t-shirt, which some may recognize, as I wore it to the lab last Thursday.

So, what is BioKM anyway?

In a nutshell, BioKM is an online lab management solution geared towards academic research labs.

Do you want to know a little more? Do you want to see if BioKM can help you organize your projects and experiments? Sign up for their free webinar next Thursday and see for yourself!
Avi Wener will review the laboratory management system and explain its benefits as well as demonstrate its ease of use.




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Thursday, September 3, 2009

Cell Press: Enhanced SnapShot




We've talked about a feature called SnapShot before (handy one-page reference guides for important topics in cell and molecular biology, see here) and now Cell Press delights us with an upgrade: Enhanced SnapShot.

Enhanced SnapShots include features only possible online—animations, embedded captions, and dynamic visuals—all accessible by the click of a mouse. The goal of an Enhanced SnapShot is to provide everything currently available with the print SnapShot plus additional layers of information that are accessible through an easy to navigate webpage.


You can check some of the capabilities of this new format here.

Making full use of the capabilities of the internet in SnapShots, comes in line with the idea behind another Cell Press idea: the Article of the Future, which we've discussed before.


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Wednesday, May 6, 2009

On Faculty of 1000 Biology



I'm surprised there are still people in my school and particularly my field of work (molecular biology) that don't know what Faculty of 1000 is. Not because I think it's a great idea (which I do), or because I think it will be a life changing experience for them to know about it (although I know they could somehow benefit from it), but because it's so widespread (if you search for papers once in a while) that it's hard to imagine that they have NEVER EVER come across with this logo before: .


Ok, maybe they have, but don't know what it is.

Anyway, (from Wikipedia):

Faculty of 1000 is a website for scientists, that provides rankings and commentary on current scientific research papers. The service is designed to act as a filter, highlighting the most significant research along with evaluations of the research written by other scientists that emphasize why a particular research paper is interesting or important.

Faculty of 1000 currently exists as two sister sites:

Faculty of 1000 Biology is an online awareness service for biologists. It is produced by a panel of over 2000 biological researchers, who regularly identify and evaluate the research articles that they have found most interesting in the recently published literature.

The other one, is Faculty of 1000 Medicine.

I usually keep an eye on Faculty of 1000 Biology which is right up my alley. It is greatly organized into areas such us Biochemistry, Bioinformatics, Biotechnology, Cancer Biology, Cardiovascular Biology, Cell Biology, Chemical Biology, Developmental Biology, etc (I just chose the first 7 of the alphabetically arranged list of areas), so you can search within your field of interest for what renowned scientists have selected as great papers.

So, how does it work? Scientists from all over the world, experts in particular areas of biology were invited to participate; to select papers they consider of interest1. In fact, "Faculty members are asked to evaluate and comment on the most interesting papers they read each month".
First, they write a short comment about it, mainly explaining why they have considered this paper and the main findings. They later rate the article (as Recommended, Must Read or Exceptional)2 and then classify it into any of seven paper types:

New finding
Technical advance
Interesting hypothesis
Important confirmation
Controversial findings
Refutation
Novel Drug Target

Finally, they classify it into one of the categories, like the ones I just mentioned (Biochemistry, Bioinformatics, etc) and the article is posted at the F1000 website.

Charles F Stevens at The Salk Institute, California said:
The Faculty of 1000 Biology is the most radical publishing idea of recent times. It is much more rational to judge papers individually than to judge them by the impact factor of the journal in which they are published. ”
Ok, so this doesn't say much, anyway. Anyone who rates an article (before reading it) based on the impact factor of the journal where it is published, is downright silly (not to say anything else).

As I mentioned a few week ago [Are we training pit bulls to review our manuscripts?]:
"(...) This will also teach them (if you haven’t told your students already) two things: 1) not everything you find in CNS journals (Cell, Nature, Science and in other one-word-title journals) is true and 2) just because a journal has low impact factor it does not mean that articles published there are weak and should not be considered in your research (...)"
Anyway, the idea behind Faculty of 1000 Biology is good, and you should check it out sometime.

For me, it has become one of my go-to sites during my downtime at the lab [Are you looking for something to do during your downtime? Check Tid Bits, Downtime Edition]


1 Sort of what we do here at MolBio Research Highlights.... or maybe, (and more accurately), we sort of do what they do :-P
2 For more info on the rating system check this.

Icons are from the F1000 website.

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Monday, March 30, 2009

Mendeley - Academic software for research papers




Do you hate it when Mac users brag about using Papers? Do you use a PC but also want a great reference managing software?

Mendeley is a free, award-winning, desktop and web solution designed for managing and sharing research papers, discovering research data and collaborating online. It combines Mendeley Desktop, an easy-to-use PDF and reference management application (available for Windows, Mac and Linux) with Mendeley Web, an online social network for researchers.
(From wikipedia)

I know that lots of fellow researchers/bloggers have talked about Mendeley, but I feel it deserves to be seen by everyone.
This is a great aid for managing articles and also for creating references lists, as it easily integrates with Microsoft Word. You can also just drag-n-drop a PDF article into Mendeley and it automatically extracts all the metadata (authors, pages, journal, etc.). But what if the metadata is incomplete? Well, you just enter the PMID of the article, and Mendeley will find the info and add it!!
Also it has several web-based features that deserve checking out, for example, data sharing, online networking, etc.

Test it... it's great, and it's free! Visit it's website now.

Here's a screenshot:



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