Commonly used software

by Walter G. Gonzalez

Posted on July 27, 2015 at 7:16 PM updated: 08/05/2015 12:25 PM

Tags: Publications

This is a list of software I use for data acquisition, analysis as well as other software which I am proficient with.


Installation and basic execution protocol videos will be uploaded soon!


Origin 8.0: I use this software to do all my plotting for manuscripts as well as for data analysis of large datasets. However, I have noticed that often when working with multiple datasets with over 20K data points origin tends to crash. For these files I either use excel or work in multiple origin projects. However, the graphing options on origin are far superior to those of excel and with just a couple of click a manuscript ready image can be obtained.


Globals for spectroscopy: designed by the laboratory of fluorescence dynamics at UC Irvine, this software package is indispensable in our lab for the day to day analysis of fluorescence intensity and anisotropy decay data. It permits the analysis of multiple file formats and more importantly, it allows the user to perform global analysis (multiple files/experiments) which significantly increases the confidence level of the recovered parameters. Even though the software is stable during analysis of lifetime decays, I have observed that analysis of anisotropy decay in the frequency domain requires a lot of tweaking to work properly running on Windows 7.


SedPhat: developed by the NIH, this software permits the global analysis of ITC (isothermal calorimetry) data as well as many other techniques (ultracentrifugation, kinetics, etc.). It is a robust software package which I often use to analyze complex ITC isotherms. The main advantage is that it provides numerous error analysis tools as well as a wide variety of binding and decay models. However, one of the main disadvantages is the lack of detailed tutorials on the use of the many variables that can be used. I believe it is a good complement to the Origin 7.0 analysis package provided by Microcal.


Fedora 20: Despite carrying most of my data analysis in a Windows 7 machine, I find the LINUX platform much better for performing molecular dynamics simulations. I particularly picked Fedora 20 because it provides good driver support for the custom made CPU-GPU workstations I built. Despite this distro having an appealing user interface, most of my work is done on terminal code.


VMD: developed by the theoretical and computational biophysics group at the Beckman Institute of Illinois University Urbana-Champaign. VMD is a powerful software package that allows very simple set-up of molecular dynamics simulations as well as trajectory analysis. Even though it is supported by many operating systems (Windows, MAC and LINUX) I have observed that loading simulations and data analysis on Windows is much slower than LINUX. The package also comes with many analysis tools and new plugins are easy to install. Additionally, VMD allows for fast and intuitive graphical representation of protein structures and video creation.


NAMD: created by the developers of VMD can easily be downloaded and executed in terminal mode in many OS. This program is in charge of actually performing the molecular dynamics simulation from scripts created by the user. Versions above 2.9 provide GPU acceleration on all OS platforms.


GROMACS: developed by the Science for Life Laboratory in Stockholm, Sweden and maintained by many other groups around the world, GROMACS is designed to perform molecular dynamics simulations as well as trajectory analysis. However, the installation can be a bit more involved than VMD/NAMD and all the protocols are executed in terminal mode which can be a bit daunting for the beginner. Nonetheless, I have found that GROMACS provides easier access to more force fields (especially for coarse grained simulations), and it also has some analysis features not available in VMD by default. I have only executed this program in LINUX and based on the GROMACS website, the Windows installation is a lot more involved.


YASARA: last but not least, this software package developed by Elmar Krieger at YASARA Biosciences GmbH, is a simple to use program that can run on many OS platforms. It was one of the first MD programs I used in the lab and it provides very robust and simple routines to perform MD simulations. I highly recommend this to anyone who wants to perform some quick simulations of small systems. However, there is a license fee and the software does not take advantage of GPU calculations, nonetheless due to the use of Amber force fields it can perform quite well. Overall, YASARA has many great tools such as alignment, minimization, membrane building and pH control as well as a very “nice looking” interface, but the lack of GPU support make it very prohibitive in running large system simulations.


ImageJ: this is one of the most widely used packages for image analysis, especially in the fluorescence microscopy field. Developed by the NIH, this software was one of the first to allow microscopy images to be analyzed extensively and continues to be updates by numerous groups across the world. Special macros can be implemented in order to analyze much more complex 3D images.


Cary50: this simple software is utilized in a day to day basis to analyze the UV-vis data in real-time in the Car50 UV-vis spectrophotometer. Further data analysis is usually carried out in excel or origin 8.0 using a csv exported file.


Vinci: developed by ISS to configure the PC1-ChronosFD custom spectrofluorometer in our lab, this software also provides a very robust data analysis package. The analysis software can be used extract lifetime and anisotropy decay parameters but it lacks the option to conduct global analysis which is often needed for complex decay patterns. Nonetheless, its stability is much superior to that of the Globals package.


Data Analysis 4.3: developed by Bruker Daltonics GmbH this software provides facile data analysis of mass spectra generated by the maXis impact Q-ToF mass spectrometer used in TIMS-MS experiments at the laboratory of Dr. Fernandez-Lima. I use this software in order to identify molecular ions in the MS spectra and assign their ligand bound and oligomerization state.


MATLAB: developed by MathWorks this software is common in many research labs due its advance graph generation protocols as well as its easy to use code syntax. I often used it to generate 3D plots as well as to manipulate complex matrix data and conduct matrix computations.


Microsoft Excel, Word and PowerPoint: nowadays these are common software and despite most people recommend not listing them, I believe they deserve proper mention.


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