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Software and Online Tools

5 Digital Tools to Increase Your Productivity in Research

Scientific research is a constant battle against time. Whether it is your Masters, PhD or Postdoc, you always feel the pressure to generate data for external validation. For that, you need to spend your time on the bench and not at the desk, but that can be hard. Unfortunately, non-laboratory tasks occupy a large segment…

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Crafting Multi-panel Images Into Figures

So, you’ve slaved away in the lab for months and now you’re ready to create your first figure –whether it’s for a thesis or a journal – way to go you! Now you could always use Word or PowerPoint to compile your first image, but don’t – ever do that! (And if you plan to…

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Resources for Becoming a Programming Biologist

Have you ever entertained the idea of learning to program? Have you tried but felt discouraged by the overwhelming amount of information out there? If you answered yes to both of those questions, I encourage you to try again with the following resources. Computer science is one of the best subjects to self learn.  …

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Brushing up on your excel skills, part 3

Having brushed up on our referencing, constructing calculations and basic functions, let’s move on to some intermediate functions that could potentially save you time and hassle in the lab. First up, filling! Filling Filling is my new favourite useful function in Excel, one that admittedly I didn’t know existed until very recently, but I’m making…

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BLAST OFF! The Basic Local Alignment Search Tool Explained

BLAST is the most popular bioinformatics online tool. But in order to properly use it, you have to understand that is not just a search query against a database but something far more complicated, and the information you get back far more…precious!

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Online Schools for Learning How to Play in the R Coding Arena

So, you come from a non-coding background, but given the rapid growth of your research results, you have accrued a pile of data that needs data mining. Now, you can leave this to your bioinformatics core facility, but if you’re curious to understand how they arrive at their conclusions (or you don’t have a BI…

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Harness the Power of BioEdit and Microsoft Excel for Quick BLAST Summaries

Basic Local Alignment Search Tool (BLAST) remains the cornerstone of biological sequence analysis. When users have one or few queries, the data are easy to interpret based on the graphical output that the search provides. However, when you have to analyze hundreds or a few thousand queries, running graphical outputs can be computationally intensive, difficult…

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How Bitesize Bio Gets Progressive Companies to Help You, the Working Scientist

Abstract: Whether it’s equipment costing hundreds of thousands of dollars and requiring millions of dollars in R&D investments or standardized kits that relieve you of tedious grunt work day in and day out, you rely on the support of companies like our sponsors to provide you with the equipment and supplies you need. But beyond…

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Brushing Up On Your Excel Skills: Part Two

Last time we brushed up on cell referencing and constructing formulae to use Excel for some basic and some slightly more advanced calculations. This time we’re going to move on to using some built-in Excel functions and go through how to apply all that we’ve done so far to a worked example that is relevant…

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Brushing Up On Your Excel Skills: Part One

Microsoft Excel can be a really powerful, useful tool for certain kinds of data processing and record keeping, and the chances are you probably don’t even know how to use half of the functions it comes with! That’s OK, personally, I find Excel a bit less user-friendly than Word, but also it’s a programme I…

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My 10 Favorite R Packages and the Cool Things You Can Do with Them

One of the best parts of R is how extensible it is. Over the years, the community has put together hundreds (thousands?) of amazing packages to make your workflow easier. The downside of this wealth is that it can be hard to find packages that do exactly what you want! Therefore, I’ve put together a…

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The 9 Online Calculators You Need to Know About

When you think of a “calculator”, you probably think of the plastic gadget in your lab desk drawer or an app that came with your phone. But there are so many helpful calculators online that do a lot more than just add and subtract numbers. Here is a list of some of the wonderfully convenient…

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Making the Most Out of Your Data with a Digital Lab Book

You will learn: How using an Electronic Lab Notebook will skyrocket your productivity Some of the features of Labfolder that will make your life in the lab dramatically easier How you can use Labfolder for free (yes, free!) and make sure you never lose any data again Summary: Keeping track of protocols, data and notes…

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How Does BLAST Work?

More than a pun on the explosive growth of sequencing data, BLAST makes annotation and comparisons of similar sequences much easier. Created by a group at the U.S. National Center for Biotechnology Information in 1991, the Basic Local Alignment Search Tool is arguably the most heavily used tool for sequence analysis (that’s available for free,…

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10 Favorite Online Tools for Molecular Biology

What did we do before the internet? And where would we be without handy online molecular biology tools? Apparently in the ‘olden days’ doing a simple gene or protein alignment required programs that used dynamic programming algorithms such as the Needleman-Wunsch and Smith-Waterman algorithms. These required long processing times and the use of supercomputers or…

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The Beginner’s Guide to LaTeX

For those of you who read the previous post about LaTeX and are interested in giving it a go, but just don’t know where to start, this article should get you on your feet. I used LaTeX to write my thesis and was (mostly) self taught, so I know how scary it is to begin…

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4 Great Websites for Bench Scientists

Friends and colleagues are excellent sources of scientific information. The Internet is too, because it is a virtual library at your fingertips. If you are looking for a great solution to a common problem (i.e. how to eliminate RNAse contamination in a laboratory), the information is waiting for you. For help with more difficult problems…

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Bio-Software for Linux

After Peter’s Introduction to Linux, those of you brave enough to accept the challenge will now have Linux installed on your machine so today I want to highlight to you some of the wonderful free software that is available for biologists using Linux. Before I start, I should mention that virtually all tools of modern…

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Free Online Bioinformatics Tools

PapersIn recognition of a fresh new year and a fresh new direction for Bitesize Bio, I thought I’d start my tenure as the fresh new Bioinformatics “guru” by introducing you to a handful of websites that will help you locate established as well as fresh new and (mostly) free online molecular biology and bioinformatics databases…

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10 links: Free Mac Software for Molecular Biologists

I’ve put together this list of 10 pieces of free molecular biology software for Macs. I hope you will find at least some of it useful. If any of your favorite free programs are not included, please email me and I’ll add them or you can leave a comment with a link. If you are…

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