Blog Archives

Free online storage space

4/25/2012

There are a variety of free online storage space that you can use. Here are the most popular examples:

Google Drive:
5GB free, up to 16TB with subscription
PC and Mac

DropBox:
2GB free, up to 16TB with subscription
PC and Mac, also available in Linux

Skydrive (Microsoft):
7GB free
PC and Mac

iCloud (Apple)
5GB free
PC and Mac

What is the best storage option?
Here is a nice article that compares all of the Cloud services.

Zoe

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PLoS Computational Biology: Ten Simple Rules

4/24/2012

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This is a link to a very useful collection of articles written by PLoS Computational Biology Editor-in-Chief Philip E Bourne and collaborators, including:

Ten Simple Rules for Starting a Company

Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia

Ten Simple Rules for Choosing between Industry and Academia

Ten Simple Rules for Graduate Students

Ten Simple Rules for Getting Grants

and many others!

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Command to get classical view (Desktop) in ubuntu

4/20/2012

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To get a classical Desktop in a newer Ubuntu version (above 11) type

sudo apt-get install gnome-panel

If gnome-panel is already installed in your desktop, then to load it you will need to logout of your account and click on the settings icon on your login name, then choose the interface you would like to use.

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Keeping up with the current literature using Google Reader

4/6/2012

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All lab group members should keep up to date with current literature in our field such as

J Chem Theory Comput
JACS
J Phys Chem B
J Med Chem
Angewandte Chemie IE

Google Reader offers an easy way to read titles + graphical abstracts of all the publications in one go. Follow these steps:

Get a google account
Login into Google Reader
Go to your favorite journal's page and look for a link called "RSS FEED". Copy that link location.
In Google Reader click on "Subscribe" and paste the link you copied above.
Now you are subscribe to that journal's updates: If you do not click on an article as you scroll down the titles, the title will disappear. You can mark an abstract as "unread" if you want to keep it in your list.
You can also link to other interesting webpages, ie our lab's blog RSS feed link is: http://www.drugdesign.gr/1/feed

So here is how Google Reader should look like:

Below is a 1-min video on how to use Google Reader. Enjoy reading!

Zoe

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2012 benchmarks of large biomolecular systems on HPC platforms

4/5/2012

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The Computational Biology group in the Computational Science and Engineering Department of the Science and Technology Facilities Council (UK) has released the third benchmarking report (March 2012) on (large) biomolecular systems carried out on various HPC platforms. Five MD codes (AMBER, CHARMM, GROMACS, LAMMPS and NAMD) have been tested on five protein and protein-membrane systems ranging from 20 thousand to 3 million atoms. Please find the report on http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx where the raw runtime data are also provided.

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Acrobat Reader X - allows you to make notes and highlight text

4/5/2012

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The new version of Adobe Acrobat Reader X has new functionalities! Unfortunately it is available only in Windows for now, but you can use your Virtualbox to comment on your PDFs - the commented PDFs appear also on the linux version of Adobe Acroread.

Review and mark up PDF files using a complete set of familiar commenting tools, including sticky note and highlighter tools, lines, and stamps. Easily compile all documents in a single PDF document.
Reuse content from PDF documents to get a head start on new projects. Save PDF files as Microsoft Word or Excel files and retain layout, fonts, formatting, and tables.
Scan and convert paper documents and forms to PDF. Make scanned text searchable automatically with OCR, then check and fix suspected errors. Search and reuse document content.

Zoe

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How to fix problem after changing IP address in Ubuntu

4/3/2012

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First, we need to install aptitude in case we don't have it
sudo apt-get install aptitude

Then,
sudo aptitude show ssh
to see if the openssh-server is installed (on our new PCs it wasn't after installing Ubuntu)

Install openssh-server:
sudo aptitude install openssh-server

ifconfig and check if the IP address in the eth0 connection is the same as in the IPv4 setting in the gui (it wasn't in the case of the new PCs)

Enable networking by right-clicking on the network icon at the top of the desktop.

Restart network manager
sudo service network-manager restart

Now, the IP from ifconfig and from the IPv4 settings should be the same and ssh should work.

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Free online storage space

Zoe

PLoS Computational Biology: Ten Simple Rules

Command to get classical view (Desktop) in ubuntu

Keeping up with the current literature using Google Reader

Zoe

2012 benchmarks of large biomolecular systems on HPC platforms

Acrobat Reader X - allows you to make notes and highlight text

Zoe

How to fix problem after changing IP address in Ubuntu

Alexis, Michalis, Danai, Panos, Sotiris, Nastazia, Vassilis, Zoe

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