Zambezi Task Timer helps you time yourself while you work (or play)

Your day consists of wet and dry duties. You shuttle back and forth between your computer in the office and your bench, sometimes annoying your workmates because your timer on the bench runs itself out before you can get to it. You need to have a timer on your PC to remind you of the things you are doing back at the bench. It would be great of that timer allows you to label your tasks, has both countup and countdown functions, can time breaks and can perform additional operations such as locking your workstation, shutting down your pc or getting to sleep. One such timer is Zambezi Task Timer from yours truly.

Download it free from here.

Sumatra PDF remembers where you left off

There are a number of alternatives for the (in)famous acrobat reader, but if you read long documents like ebooks on your computer, consider Sumatra.

Sumatra is small, fast and, if you are a touchscreen user, has a friendly full screen view. But my favorite feature is its ability to remember where I left off in the document I was reading, so I don’t have to scroll down looking. Easy way to get through all those long papers, theses or texts you have gathered on your pc (assuming of course they are in PDF format). Try SUMATRA. You may like it.

Use Google Reader to track your favorite journals

You probably know that you can use Google Reader to track your favorite sites and blogs (like this one). If you are not familiar with Google Reader, you really probably should be. Google Reader is a web aggregator. You can add your news sites and blogs and Reader will update with new content and let you know what you have read and what you haven’t.  Less mentioned for researchers is how you can utilize Google Reader to track your favorite journals. You can add journals like Plant Physiology, Nature, Science, PNAS etc to your reader subscriptions to get the latest content from them.

Try out Google Reader for your scientific journals. Best way to stay up to speed.

Online tools for biologists

If you do cloning work, you will probably need to add these tools to your bookmarks. I recommend creating a folder for these if you use a bookmark toolbar. Write us or drop a comment if your favorite tool is missing from the list.

NCBI BLAST

The Basic Local Alignment Search Tool (BLAST) at the NCBI website is perhaps the most popular online destination for molecular biologists. With BLAST you can compare your sequence to database sequences so you can find regions of similarity. Click here to go to BLAST.

ClustalW2

Hosted at the European Bioinformatics Institute website, ClustalW2 is a sequence alignment program useful when you have a number of sequences and you want to, well, align them to find regions of similarity. Unlike BLAST, with ClustalW2 you are comparing your own sequences, not your sequence against a database.

ExPASy Translate tool

Translates your nucleotide sequence into a protein sequence. Visit ExPASy.

Reverse Translate

If you have a protein sequence and you want to reverse translate it to the nucleotide sequence, Reverse Translate is your tool.

Reverse Compliment

This comes in handy when you are designing primers. Reverse Compliment does as its name suggest – it reverses your sequence and compliments it. You can also change settings if you only want to reverse without complimenting or to compliment without reversing. It is a nice bookmark for researchers.

Reverse Translate and Reverse Compliment are hosted at bioinformatics.org

NEBcutter

This is a handy tool for cloning work. NEBcutter allows you to check for restriction enzymes that cut your sequence only once. You can “custom digest” your sequence to check if specific restiction sites exist on your sequence.  Worth mentioning while we are at NEB is their Double Digest Finder, which allows you to check if the two restriction enzymes you will be using can actually work together in a double digestion (in my defense, English is my second language).

OligoAnalyzer

From Integrated DNA Technologies, OligoAnalyzer analyzes your primers for Tm, hairpins, self-dimers etc.

Primer3

This is your primer design tool for picking primers from a DNA sequence. The website is rather cluttered but the tool is nifty enough.

Get quick specific facts from Wolfram Alpha

You use a search engine (Google, Yahoo, Bing etc) to look for information. The search engine gives you links related to your search input and you go through them to see if you can hit on exactly what you want. This works very well most of the time. But sometimes you just need specific answers not links. Lets say you want some quick facts about the sodium sulfide. You could punch it into Google or bing and get a list of links which require further checking to get what you want, or you could enter your search into Wolfram Alpha and get specific summary about sodium sulfide. Click here to see what I mean (this will actually execute the search in wolfram alpha).

Wolfram Alpha is an answer engine unlike search engines like Google and Bing. If you use firefox, there is an addon that allows you to get Wolfram Alpha results within a google search. You can find it here.

Enjoy.

Simplify your lab calculations with Lab Calculator

In your routine work in the lab you prepare stock solutions, use prepared stocks, and play around with various unit conversions. That means you should be competent with basic lab math, which is not too hard. but it is too important and you don’t want to make mistakes in a stock you will be using for the next three months. The Lab Calculator is a small utility that helps you with these basic calculations. You can

• calculate the mass of a chemical required to make a stock solution of your choice
• calculate the final concentration achieved by dissolving a given mass in a given volume of solvent
• perform a basic dilution
• perform the famous C1V1=C2V2 calculation (where C1 is stock concentration and V1 is volume of stock, and C2 is final concentration and V2 is final volume).

You can even get help with handling basic ratios like how much water to add to 346ml of 95% ethanol to get 70%. The Lab Calculator is free, and the current version is 1.30. Since it is developed by yours truly, you can email me with comments. Click here to visit the Lab Calculator homepage.

Organize academic publications with Mendeley Desktop

You have been downloading academic publications for the past couple of years like your life depended on it (well, your life actually depended on it). Now there are hundreds of them on your hard drive and you have difficulty in finding a paper when you need one. So you download it again. Before you know it, you have five copies of the same paper on your computer and you still can’t find it easily when you want because, well, you saved it with the default file name when you got it online and the default file name is something crazy like a string of numbers. Well, worry not. The guys over at Mendeley Research Networks have you covered. Mendeley Desktop is a desktop (duh) application for organizing your academic papers. It automatically extracts document details (name of journal, title, year of publication etc). So from that useless string of numbers that you called a filename, you now have something you can use. That way, it’s easy to spot multiple copies of the same paper. But that is not all you get. Mendeley Desktop features a lightning fast (alright, its fast) live search in your library so you can retrieve the paper you want quickly. Once you start using it, you will wonder how you ever went through those years without it. It runs on Windows, Mac and Linux so no child is left behind. Oh and one more thing; it has a really cool native PDF reader that works well.  You can still launch your paper with your external viewer though.

A screenshot of Mendely Desktop on my pc. If you double click any one of the papers, it will open the paper in the native reader as show below:

Mendeley Desktop is a must have for graduate students and post docs. To check it out, click here (Mendeley Desktop is still in it’s Beta, though it works really fine. It is FREE, but you will be required to register).

Keep everything in one place with Microsoft OneNote

We will be talking about software for making your experience in the lab more productive - or, failure of that, just a tad more interesting. You can, of course email me or send comments on your favorite toys that make your work easier. If you don't, I will just write what I want anyway, which was the original plan.

I decided to start off by talking about my favorite application of all time - Microsoft OneNote. OneNote is your one stop for all your notes, lists, ideas etc. For me, it is the one application (outside of system and security software) that is always running on my pc (which is conveniently tablet, so I can handwrite). OneNote allows you to open several notebooks, create different sections within a notebook and pages within a section (see below). This makes navigation very easy.

OneNote’s functionality is even great for surfing. While surfing the web, you can paste information of interest into your OneNote (rather than saving web pages, which is really old school). If you are trying the Office 2010 beta (you can find it here), you will notice that OneNote 2010 has a docking feature which allows you to dock it to the desktop, so that you can drag and drop stuff from other applications (mostly you will like to do this while surfing). If you get into the habit of throwing things into your OneNote portal (and then going through them end of week when you, hopefully, review your week), very few things will slip through your fingers. One of the things you will like about OneNote is that once you type (or paste) something in, it is there - no need to save.

If you haven't tried it yet, give OneNote a try. OneNote is part of the Microsoft office suite and is not free. The 2010 beta is free until October 2010.