Software Preparation for the 2015 Interdisciplinary Quantitative Biology Boot Camp
Please examine the following list to learn about the software that will be needed for many of the hands-on computational events at
Boot Camp. You will need to download the software BEFORE coming to the various sessions (indicated with icons on the program).
Please check this site again shortly before boot camp, as there may be updates. If you have any questions, please contact the
Proteomics technical support staff.
Laptops:
Your laptop computer can be Windows, Mac, or Linux. There are plenty of outlets available in Proteomics room 120, so feel free to
bring a power supply cord.
Widely used software needs:
1. A Web browser – Needed to navigate to websites. Good choices are Firefox, Google Chrome, Safari, and Internet Explorer.
2. A text editor – Needed to open text files and modify them. Any text editor will suffice.
3. Java – Needed for many of the computational workshops and talks
Java is a computer programming language designed to facilitate application development, particularly for web applications.
You will need the Java version 1.7 (or a more recent version) installed on your computer.
To install Java:
a. If your web browser or operating system has a "check for updates" option, allow it to run and install any
updates it offers.
b. Go to java.com
c. Follow the prompts and instructions for your operating system and browser.
d. Try the steps above to test Java again.
To check if your computer has Java software installed already:
a. Go to rscb.org
b. Look for any warning messages or requests for permission and allow the browser to start Java. If you are
asked to allow – click on the allow button
c. Wait a few seconds, scroll down a bit, and you should see a square black box with a multicolored
molecular structure which you can rotate with your mouse. Success! You have Java installed.
d. If you don't see a molecule after acknowledging all warnings and waiting for half a minute, try installing
Java yourself.
Workshop software needs:
1. Bioinformatics Workshop
Useful websites: To be provided soon
2. Foldit
1.
2.
3.
4.
Foldit is a program that provides a game format for manipulating protein structures. If you have any questions, please
contact kristin.blacklock 'at'rutgers.edu. Your laptop computer (Windows, Mac, or Linux) should be able to run a currentgeneration web browser such as Firefox, Google Chrome, Safari, or Internet Explorer.
Obtain a Rosetta Software Academic License
a)
Visit the website.
b)
Enter your details and click on 'Execute License'.
Create a Foldit account:
a)
Visit the website.
b)
Click on ‘Create new account’.
c)
Enter your information in the next page to create an account.
Download Foldit software:
a)
Download and install BOTH versions of Foldit below for your operating system:
(1) Mac OS X (10.7 or higher): Foldit-osx_x86.zip and FolditInternal-osx.zip
(2) Windows: Foldit-win_x86.exe and FolditInternal-win.exe
(3) Linux: Foldit-linux_x64.tar.gz and FolditInternal-linux.tar.gz
b)
Open or execute the file to install and use the Foldit software. If you have trouble with dependencies in Linux
please contact us.
Download data files for Boot Camp tutorial:
a)
Option A: Download the zip file and extract the contents.
(1) foldit-structures-bootcamp.zip
Option B: Download the data files individually.
(1) 1GFL_atoms.pdb
(2) 1GFL_CH6.enzdes.cst
(3) 1GFL_CH6.params
(4) 2H5Q_atoms.pdb
(5) 2H5Q_CH6.enzdes.cst
(6) 2H5Q_CH6.params
(7) TrpCage_extended.pdb
(8) TrpCage.second.pdb
Start Foldit software:
a)
Double click on the FolditInternal icon (an automatic update may begin).
b)
If you previously created a Foldit account, enter your Username and Password. If not, proceed to the next step.
c)
Click ‘Play Online’.
i) If you are unable to connect, click ‘Play Offline’. If prompted, click ‘Yes’.
Load PDB files:
a)
Click on ‘Intro Puzzles’, then Level 1-1.
b)
Press ‘Ctrl’, ‘Alt’, ‘Shift’ and ‘A’ in this order.
i) This should open a window with your directory structure such as a Finder window (MacOS) or Explorer (Windows).
c)
Select the TrpCage_extended.pdb and click ‘Open’.
i) To open a PDB file with supporting files, such as constraint (.cst) and parameters (.params) files, select all the files
at the same time before clicking ‘Open’.
Exit the program
a)
Click the ‘Menu’ Tab at the bottom of the Foldit window.
b)
Click on the ‘Save and Exit’ icon. Click ‘Yes’ when prompted.
OR you can also click the (x) at the top of the window, like normal.
b)
5.
6.
7.
3. Protein Visualization, Analysis & Comparison AND Exploring Macromolecular Structures
A. Chimera (version 1.10)
This software is free for academic use.
Windows, Mac, Linux: download, tutorials
Download: Visualizn-data, Exploring-FPs, Visualization-wksheet
C. Useful websites:
1. RCSB PDB database: http://www.rcsb.org/
2. Expasy translating tool: http://web.expasy.org/translate/
3. Expasy Peptide Mass tool: http://web.expasy.org/peptide_mass/
4. Expasy tool for multiple sequence alignments: http://embnet.vital-it.ch/software/ClustalW.html
5. Protein Sequence Comparison tool: http://www.cbrg.ethz.ch/services/PhylogeneticTree
6. UniProt database: http://www.uniprot.org/)
 e.g., native green fluorescent protein: http://www.uniprot.org/uniprot/P42212
7. Ligand-expo database: http://ligand-expo.rcsb.org/
8. Two-dimensional diagrams of complexes: http://poseview.zbh.uni-hamburg.de/
9. Ligand explorer visualization: http://www.rcsb.org/pdb/staticHelp.do?p=help/viewers/ligandExplorer_viewer.html
10. Nucleic acid database: http://ndbserver.rutgers.edu/
11. Unified Data Resource for 3-Dimensional Electron Microscopy: http://www.emdatabank.org/
D. Additional useful resources:
1. Pymol: a molecular visualization system: http://www.pymol.org/
2. Coot: software for visualized of the electron density: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
4. Amber Boot Camp Project
Amber is a software package for performing molecular dynamics simulations of proteins and nucleic acids. The Amber Boot
Camp Project will consist of two consecutive sessions.
Note: what we are attempting here is more ambitious (and hence harder) than downloading an executable code like
Chimera and others discussed above. You will be installing and running a virtual Linux machine on your laptop. You will
need a laptop with at least 4 Gbytes of main memory and 10 Gb of free disk space. If your laptop computer does not have
these features, there are a number of other computers available for use. If this applies to you, contact Proteomics technical
support staff to make special arrangements. Once we know who is signed up for the Amber project, we will email detailed
instructions about what you can do before the boot camp begins. The virtual Linux machine will be running through
VirtualBox, which can be installed on Windows, Mac OS X, and Linux. The VirtualBox installers for Windows and Macs will
be provided to you along with the Amber-loaded Linux disk image on a memory stick, but you can save time by installing
the correct VirtualBox application for your operating system before boot camp begins. If you are using Linux, you should
install VirtualBox using your package manager (e.g., “apt-get” or “yum”).
5. DNA Cloning and Sequencing Methods Workshop AND DNA Sequencing Data Analysis
A. Benchling: Setup an account on Benchling.com (it is free). You will need to access the site to get the most out of the
class. Sequence files will be made available to you as both sequence specific files (fasta, seq,sw, etc.) as well as a text
file.
B. FinchTv: Download. You will need to register but it's free. For Mac users there is also the program 4peaks, but for
consistency we will be focused on finchtv for the classes.
C. Jalview: Download the Jalview desktop application. Requires Java to be installed (link at Jalview site if you don’t
already have it installed). Free program for multiple sequence alignment and visualization.
6. Mass Spectrometry Data Collection Workshop
X-tandem and GPM: Both programs can be installed on a windows machine with Perl:
A. Go to ftp://ftp.thegpm.org/projects/gpm/gpm-xe-installer/
B. Pick the version suitable for your computer and install.
C. Follow the directions to add a custom database (GFP.fasta) consisting of all GFP-related protein sequences used for the
Boot Camp.
1. Directions for adding the database:
https://www.dropbox.com/s/psdq9j76utezvdu/How%20to%20add%20database%20to%20GPM%20search%20eng
ine.docx?dl=0
2. The sequences to add: https://www.dropbox.com/s/63lq68nii2829wh/GFP.fasta
Useful websites:
1.
2.
A basic MS resource: http://www.ionsource.com/
A tryptic peptide prediction tool: http://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msdigest
3. An MS/MS fragment prediction tool: http://db.systemsbiology.net:8080/proteomicsToolkit/FragIonServlet.html
4. An MS isotope tool: http://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msisotope
7. X-Ray Crystallography Data Collection Workshop
ccp4: a suite of crystallographic software for structure determination, will be used for the analysis of X-ray crystallographic
data for structure solution. Participants are welcome to try using it, but this is optional.
Free Download
Useful Resources:
a. Coordinates and structure factor data for PDB entries that closely match each of the FPs from www.rcsb.org:
i. mCherry – PDB ID 2h5q
ii. mOrange – PDB ID 2h5o
iii. mCitrine – PDB ID 3dq7
iv. mCerulean – PDB ID 2wso
v. msfGFP – PDB ID 2b3p
b. SF-Tool server (http://sf-tool.rcsb.org/) to generate the electron density maps.
c. UCSF Chimera to visualize the electron density maps and atomic coordinates
d. Review article: Chudakov et al., Physiol Rev, 90: 1103–1163, 2010.
8. NMR Spectroscopy Data Collection Workshop
A suite of NMR data analysis software will be installed on a number of Macintosh computers on site at the Workshop.
If you wish to make plots with the data, it is recommended that you have Excel or another plotting program with simple
curve-fitting capabilities.
9. Differential Scanning Calorimetry
Useful resources:
a. Microcalorimetry of Macromolecules: The Physical Basis of Biological Structures- Privalov, Peter L. Wiley – 2013
Examining the physical basis of the structure of macromolecules—proteins, nucleic acids, and their complexes—
using calorimetric techniques
b.
Calorimetric Methods to Characterize the Forces Driving Macromolecular Association and Folding Processes.
Conceicao A.S.A. Minetti, Peter L. Privalov, and David P. Remeta In: Proteins in Solution and at Interfaces: Methods
and Applications in Biotechnology and Materials Science (2013): 139-177.
10. Fluorescence & Circular Dichroism (CD) Spectroscopy
Useful websites:
(1) Fluorescence spectroscopy basics: http://media.invitrogen.com.edgesuite.net/tutorials/1Intro/player.html
(2) Fluorescence spectra analysis: http://media.invitrogen.com.edgesuite.net/tutorials/2Spectra/player.html
11. Cancer Biology Tutorial
R Studio: a free software environment for statistical computing and graphics, free and available for Windows and Mac.
R is part of many Linux distributions. You should check with your Linux package management system in addition to
Following the instructions on the links below.
1. Download and install: R studio for OS X, Windows, or Linux
From http://www.rstudio.com/
2. Download and extract: Data will be provided few days before the class
3. Download slides: To be given few days before the class
Optional download: Introduction to R (pdf)
If you need help: How to install and download R Studio