The lifescience toolbox blog

:: simple :: efficient :: vital :: :: modular :: open-source :: inspiring :: :: smart :: novel :: unusual :: In a nutshell, little things that make your daily labwork easier. Enjoy! Share this blog with your labmates: :: Click here for convenient e-mail newsletter ::

[lifescience-toolbox-blog]

How to outsmart spam mails

The web it full of supposedly free stuff - e.g. newsletters, tutorials etc. The only thing you need to provide is a mail address. Of course, just to send you a confirmation mail ... and may be hundreds of spam mails in the weeks after. With a service for disposable mail, you can simply outsmart the system. Simply register using a self-destroying mail address, then hit the activation link of a respective confirmation mail and that’s it. All future spam will go nowhere.

Simply get a disposable mail address here: https://10minutemail.com

[lifescience-toolbox-blog]

Automated proofreading of data input

Assuming you did a great job during data acquisition, since you painfully learned your lesson called “Trash in, trash out”. Still your raw data can be contaminated with various grains of sand, which would ultimately prevent your analysis workflow from running smoothly (regardless if you do it manually or using a program). That’s why data PRE-processing is essential for anyone caring about high data quality. For this, the dataproofer is a super handy tool. It let’s you automatically check your incoming data with different layers of rules. Follow the link for more information...

https://github.com/dataproofer/Dataproofer

[lifescience-toolbox-blog]

Reverse engineer published plots: from pixel to datapoints

This is one really neat piece of software and it is definitely worth a bookmark in your browser. In case you were ever in need to get the underlying raw numbers that were used to generate a plot/graph, than this is your way to go. It also helps you measuring distances from microscope images and geographic maps. It basically enables you to reverse engineer a plot to get to its numerical base.

http://arohatgi.info/WebPlotDigitizer/

[lifescience-toolbox-blog]

Mobile Statistics

Did you ever need to do a quick-and-dirty statistical analysis? Like calculating a regression curve of your protein assay (while holding a pipette in one hand) or checking whether the means between two groups is indeed different (while sitting in the audience of a talk).

Then make yourself familiar with the world of “Wolfram Alpha”. This awesome platform not only provides access to heaps of curated scientific data, it also offers on-the-fly calculation of thousands of algorithms and methods. Using their mobile app, you can than even do statistical analysis without use of a regular desktop machine.

[lifescience-toolbox-blog]

Open Source Hardware

Similarly to open source software that can be freely shared/modified/improved, open source hardware gains more and more momentum. Besides being much cheaper than commercial products, DIY labware can be freely customized to perfectly fit your scientific needs. Because, let’s be honest, sometimes we just buy an expensive piece of hardware just because of one particular feature (out of hundred other functionalities that comes with it).

Long story short - the following link is an awesome resource for open source hardware. It covers things like microscopes, motorized stages, and centrifuges.

http://collections.plos.org/open-source-toolkit-hardware

[lifescience-toolbox-blog]

Structuring your project with mind maps

A common challenge for any scientific project - the longer you work on it, the more complex it gets. At some point it’s impossible to keep overview of all the sub-projects and milestones. Especially if your boss wants you to follow them up all at once. It’s literally nerve wrecking.

One solution to not drown in sub-projects is to keep an updated mind map somewhere on your computer. The software FreeMind runs on every system and allows you to easily compose mind maps. Automated folding/unfolding and links to files or to websites can tame even the most complex projects. It feels really relieving to know, that all the little details are structured and stored at one place. Just give it a try!

Here is the link: http://freemind.sourceforge.net/

[lifescience-toolbox-blog]

Impress your colleagues with DIY high-throughput analysis

“The best thing since sliced bread!”

You can know build your own pipeline of automated high throughput analysis without prior knowledge of any programing language. Using the software KNIME you can process tables/text files/images via a convenient graphical interface and re-apply the same workflow to an (almost) endless list of additional files on you hard drive. KNIME functionalities include simple tasks as sorting/filtering/combining, and goes further to calculation of data summaries, statistical tests, cluster analysis and machine learning. Higher functions such as pulling data from web databases or image processing are included as well. In case there is still a functionality missing you can import and apply a R library (known to be the most popular open-source data handling software). For impressive graphical summaries you can use the ggplot2-library from R to generate PDF-reports of your experiments.

It is definitely worth to spend some time getting familiar with the software. It will pay off very quickly. Again, regardless of the complexity of your analysis, you can save the workflow and use it as an automation template for all future experimental data. This way you can massively speed up you usual lab-workflow (and may be impress you boss and colleagues).

To get started just follow the links below:

“Getting started...” with KNIME

“Getting started...” with R within KNIME

“Getting started...” with plotting usign ggplot2

[lifescience-toolbox-blog]

"Mmmhhh... these results do not really make sense..." or let the computer have a look at your data

As your probably noticed there is currently quite a big hype about the use of Big Data collected from the internet. And isn't it unfair that all the big web companies have such big computer clusters and super-smart programs to analyze endless rows of tables? And on the other hand we, the average scientists, are stuck with just our favorite office software and nothing else but our own brain - no fancy tools that help us to make sense out of our research data? Luckily there is an incredible powerful open-source software tool that brings big data analysis right on your desktop computer.

It's called WEKA. It comes with a very friendly graphical user interface and guides you and your data through algorithms that allow for smart classification, clustering, prediction and model generation. Now you may think: "Well... I don't even have big data so far..." That's even better. WEKA helps you also to understand more simpler experimental results with just a few parameters. As a audio-visual introduction I can strongly recommend the following video created by Brandon Weinberg: 

[yellowboxshoes]

Make the most of your day! 🌻🌻🌻 #yellowbox #beYB #thursday #quote #wisdom (at www.facebook.com/yellowbox)

[lifescience-toolbox-blog]

Everyone deserves a second chance... also this guy called 'Math'

Learning and actually applying Biological Modeling has never been so easy with this new modeling software called Morpheus. It comes with a nice graphical interface and basically guides you through different options of your future mathematical model. You can very quickly model

cell growth curves including effects of growth factor consumption

multi-parametric signaling events

2D and 3D pattern formation (based on diffusive signals)

behavior of cell clusters (e.g. migration, vessel sprouting)

You can find further information by following this link: Morpeus-homepage or watch a brief video introduction here.

[lifescience-toolbox-blog]

"Oohh no... this will take forever..." or lab automation using LEGO robots

Chech out this vid and get inspired...

[lifescience-toolbox-blog]

Fastest way to prepare images for a puplication figure

... is using a great tool called FigureJ. It allows interactive scaling, cropping, alignment of raw images while keeping it in a preset format suitable for your desired journal (single vs. double columns, 300 dpi etc...). You can add/change/remove panel labels and scalebars as you like and save it for later modification. Building multi-image panels is now very easy.

I highly recommend you the following link for further information and download:

http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:figurej:start

[lifescience-toolbox-blog]

Best science-video collection ever

Just check out DNATube.com and be sure to spend the next 3 hours watching short science-vid clips.

PS: might be an option to ‘spice up' your next lab-meeting presentation (do not forget the reference). Unfortunately the download-function is inactive due to open copyright situation.

[lifescience-toolbox-blog]

Avoid WiFi-free black holes

In case your lab has poor or unstable WiFi-connection, then just use your laptop as a personalized hotspot for your smartphone, tablet etc. What you simply do is forwarding the LAN-internet (hard-wired internet) throug your laptop to a personal WiFi.

Please follow the following link for instructions using MacBooks:

http://macgroup.org/blog/2010/09/27/turn-your-macbook-into-a-wifi-hotspot/

PS: this also works nicely in Hotels with poor WiFi-networks (given you have LAN-internet in your room available)

[lifescience-toolbox-blog]

Poster inspiration

http://f1000.com/posters

[lifescience-toolbox-blog]

Communicating science by infographics

(Figure generated by http://www.tagxedo.com/app.html)

Lately infographics became a popular way of transporting information to a broad audience. It takes advantage of the fact that visual representation of scientific content is generally much easier to understand (and to memorize) than 'wordy' explanations. However it challenges the tradition of the established science community. So be careful when using the following tools. But if your poster (for example) shall stand out from the crowd - just go ahead!

Here are my favorite online-tools for creating a 'killer' poster, a surrealistic word-cloud or a visual CV:

1. THE famous online infographic tool:

http://visual.ly/

2. A cloud made of words

http://www.tagxedo.com/app.html or http://www.wordle.net/

3. The visual CV

http://vizualize.me/

[lifescience-toolbox-blog]

Collecting contents from the web easily

Nothing has changed since thousands of years - we are still hunter-gatherers! Especially if it comes to scientific protocols. A common approach is to browse the net, collect everything that looks useable for your desired purporse and afterwards determine the most promising protocol (which is usually a hybrid of multiple protocols).

For the hunting-gathering part the online tool "Evernote-Webclipper" is super handy. The browser plugi-in efficiently copies previously marked paragraphs to your evernote-account (which is an online data repository, accesible from any computer connected to the WWW). Instead of juggling hundreds of PDFs you have only the important information directly in one file.

Here is the link: http://evernote.com/webclipper