From command-line bioinformatics to bioGUI

Bioinformatics is a highly interdisciplinary field providing (bioinformatics) applications for scientists from many disciplines. Installing and starting applications on the command-line (CL) is inconvenient and/or inefficient for many scientists. Nonetheless, most methods are implemented with a command-line interface only. Providing a graphical user interface (GUI) for bioinformatics applications is one step toward routinely making CL-only applications available to more scientists and, thus, toward a more effective interdisciplinary work. With our bioGUI framework we address two main problems of using CL bioinformatics applications: First, many tools work on UNIX-systems only, while many scientists use Microsoft Windows. Second, scientists refrain from using CL tools which, however, could well support them in their research. With bioGUI install modules and templates, installing and using CL tools is made possible for most scientists—even on Windows, due to bioGUI’s support for Windows Subsystem for Linux. In addition, bioGUI templates can easily be created, making the bioGUI framework highly rewarding for developers. From the bioGUI repository it is possible to download, install and use bioinformatics tools with just a few clicks.


Yes
No 10. How easy would it be for you to use the command-line? * Here we are interested in your priorities. How much effort would it be for you to use the command-line in order to run a tool? If you do not feel distracted at all, choose "Not much/1". If you think you could manage to run a program from the command-line, but feel you could do more relevant tasks to your job, choose "3". If you think you could not use command-line tools, choose "Unable to cope with/5". Mark only one oval. 12. Why did you choose the answer above? *

Your experience with bioinformatics tools (1)
Please answer these questions with regard to a bioinformatics tool you used or wanted to use (does not mean you successfully used it! In the following section we will ask you how easy you found specific processes during the use of the bioinformatic tool. If you could not access a step (e.g. you could not run the tool, because you could not install it), please choose the "Does not apply" option.
20. Downloading/Accessing the software was easy. * Mark only one oval.

Hands-on Use-Case 1
In this use-case we want to find out how easy it is for you to use a tool on the command line.
We want you to install graphmap and align long reads to a given reference.
In preparation for this study, make sure to have downloaded the provided archive to the test computer and extract it into a folder "study1" in your home directory.
Step 1: Download and install graphmap Abort this step after 5 minutes, no matter how far you have gotten.
A Terminal has been opened for you. You are now in the 'study1' folder. Enter the following commands to install graphmap. Step 2: Using graphmap on the command line Abort this step after 5 minutes, no matter how far you have gotten.
We now have to align the reads to a reference.
Within the study1 folder there are 2 files. Enter 'ls<Enter>' in the Terminal to see them: scer_genome.fa SRR5989373.short.fastq These are the input files for the alignment. scer_genome.fa is the reference genome and SRR5989373.short.fastq are the reads.
Try to find out how to align the reads. The output file should be mapped.sam in the study1 folder.
29. How long did you take? *

Hands-on Use-Case 2
In this use-case we want to find out how easy it is for you to use a tool with bioGUI.
We want you to install graphmap and align long reads to a given reference.
In preparation for this study, make sure to have downloaded the provided archive to the test computer and extract it into a folder "study1" in your home directory.
Abort this task after 5 minutes, no matter how far you have gotten.
Step 1: Install graphmap Abort this step after 5 minutes, no matter how far you have gotten.
Locate the study1 folder and the bioGUIRelease subfolder.
Double-click on the bioGUI icon (in the bioGUIRelease subfolder) and start bioGUI.
Click on "Download Templates" and download the "Install graphmap (github)" template. Step 2: Use graphmap Abort this step after 5 minutes, no matter how far you have gotten.
We now have to align the reads to a reference.
Within the study1 folder there are 2 files: scer_genome.fa SRR5989373.short.fastq These are the input files for the alignment. scer_genome.fa is the reference genome and SRR5989373.short.fastq are the reads.
Try to find out how to align the reads. The output file should be mapped.sam in the study1 folder.
38. How long did you take? *