Tools I like


Expasy - Tons of web-based biological sequence-based tools

PDBe - Good tools for PDB mining and analysis

ViperDB - Virus capsid specific Cryo-EM and PDB database with synchronized coordinates and orientations. Also some tools for building and analysis

CNS - Old-fashioned suite for crystallography and NMR structure determination and analysis

CCP4 - Powerful suite of programs for crystal structure determination

Phenix - The present and future of macromolecular crystallography directed towards automation

PyMOL - Standard PDB viewing and rendering tool. Open source but not entirely free. Windows, OSX and Linux

Chimera - Free academic 3D model viewer and editor. Not as convenient as PyMOL but much more powerful. Windows, OSX and Linux

Coot - Visual model fitting program

RAVE -  Old school crystallography tools for symmetry operators, PDB and map editing. Includes Mapman and Moleman

ATSAS - Suite of programs for biological small-angle scattering analysis

Serial Cloner - Cross-platform free protein and nucleic acid sequence analysis, editing and in silico cloning tools

Robetta - Web-based protein structure prediction server. Probably the best there is

EMAN2 - Preferred Cryo-EM processing software

RobEM - Cryo-reconstruction processing and analysis

Relion - New age Cryo-reconstruction suite with 3D class-averaging and a bunch of other smart methods


Fiji - ImageJ with neat extensions

Regular tools: In addition to everything google,

Garageband - Apple's greatest gift

Microsoft Office - Microsoft's

Captur - Nifty screenshot capture tool for OSX

iTerm - A better terminal than OSX's default program

SmartConverter - Quick media conversion

youtube to mp3 - Listening to old movies is fun. Especially when driving through rural Indiana

SoundCloud - Share your music and listen to others

The unarchiver - Free OSX program that works with every kind of compressed file. Must have

Free and Open Source:

Gedit - There are text editing tools and there is Gedit. Enough said.

The gimp - FOSS alternative to Adobe Photoshop. Good enough for all your needs unless you are crazy advanced. No you are not

Inkscape - Like the gimp but for Adobe Illustrator

VLC - One stop player for all formats of video and music. Quick and clean.

Calibre - E-book management and viewing

LibreOffice - Fast and efficient FOSS office suite

Zotero - Started as a firefox plugin. Very good for citations and bibliography. I use it for all my technical writing

Pidgin - Simple messenger client with some nice plugins. Less noisy than Adium

Audacity - Great sound file editing tool

Firefox - The browser of choice

Scribus - Open source publishing

Android apps: Pretty much every google app is brilliant. Here are some others I recommend

Contacts+ - The ultimate unifying contacts app

TuneIn radio - Get every local radio station on your phone, as long as it is on the internet. Worth every cent of the $1 you pay for it

Brightest Flashlight - That

Viber - A phone-based, no sign-in required, alternative to Skype

Whatsapp - Free texting

Llama - If you know how to use it well, this is one of the best apps for Android. Use it to automate features on your phone based on location

Terminal Emulator - So you are never too far from a command line

Wapedia - Smooth running Wikipedia app

ScoreCenter - ESPN news, media and score updates. Try the other ESPN sport-specific apps too


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