Introduction to InsideDNA Bioinformatics Platform for Tools & Analysis

Author : InsideDNA Time : 02 July 2050 Read time : 6 min

In this short tutorial, we explain the basics of working with the InsideDNA platform. While it is very easy to work with our application and most things are self-evident, there are some nice tricks you may not know from the first log-in. With this tutorial, we want to make sure you know all these tricks and can get most of the InsideDNA functionality. We therefore strongly recommend to at least give a brief glance on this tutorial before diving into genome crunching and sequence analysis.

You can simply watch these two video tutorials. First tutorial covers basic usage of the platform and the second one - usage of the terminal.

 

 

1. Registration

Create an account on the InsideDNA website. Once you get a confirmation email, remember that you will need to fill a small survey (at most 3 minutes) and then you are ready to go.

Introduction to InsideDNA bioinformatics platform for tools & analysis login screen

2. General overview of InsideDNA

In the platform you have three main tabs in the top navigation menu: Tools, Tasks and Files. Their purpose in quite self-explanatory, but in principle:

  • In Tools you can search for bioinformatics tools, organize them into projects and run;
  • In Tasks you can monitor progress of your submitted tasks and do some operations on them;
  • In Files you can manage all your data pretty much like in any normal desktop file manager

Introduction to InsideDNA bioinformatics platform for tools & analysis overview screen having all tabs

3. Search for tools

There is a very powerful searching engine behind InsideDNA tool database which makes it easy to discover not only packages, but rather specific functions within software that suites your needs. To search for a tool simply use search field in My tools and type any keyword that maybe relevant to your query.

Introduction to InsideDNA bioinformatics platform for tools & analysis screach screen

The  results can be presented in a thumbnails view:

Introduction to InsideDNA bioinformatics platform for tools & analysis result screen: thumbnail

Or in a table view:

Introduction to InsideDNA bioinformatics platform for tools & analysis result screen view in form of tables

Moreover, you can always subset your search results by specific keywords or keywords combinations.

Introduction to InsideDNA bioinformatics platform for tools & analysis drill down search with keyword

When you find a tool that looks interesting, you can obtain more information about the tool by pressing Read More button.

Introduction to InsideDNA bioinformatics platform for tools & analysis tool infromation screen

Later we will enable sorting by various columns so you can easily summarize the search results.

4. Create a new Project

It is very handy to organize tools by projects, because it is then much easier to find which tools and with what settings you used – thus, your research becomes more reproducible and easy to understand even for yourself a couple of weeks later.

To create a new empty project click on +Add new project.

Introduction to InsideDNA bioinformatics platform for tools & analysis new project creation tab screen

And select a Project name

Introduction to InsideDNA bioinformatics platform for tools & analysis new project name selection field shown

5. Add tools to Project

You can always add tools into projects. For example, type in the search box: TopHat2, then click on + button and choose Arabidopsis project in the dropdown list.

Introduction to InsideDNA bioinformatics platform for tools & analysis add tools option screen

6. Initialize a task

To run a tool, you need to initialize Tool settings menu by clicking on Run Tool on a tool thumbnail.

Introduction to InsideDNA bioinformatics platform for tools & analysis initialize tool screen by run

7. Specify Tool settings

Once you clicked on Run Tool, you will have a Tool Settings menu opened. Here you need to specify the Task name, tool parameters and so-called queue. Then you will need to preview the task and submit it.

Specify the task name which will make sense for your later on.

Introduction to InsideDNA bioinformatics platform for tools & analysis task name field

Clicking on the Browse button will open a mini File Manager (miniFM) that facilitates the choice of input/output files/folders.

Introduction to InsideDNA bioinformatics platform for tools & analysis mini file manager screen

There you can also create a new folder and navigate in your datasets

Introduction to InsideDNA bioinformatics platform for tools & analysis new folder screen

It is a good idea to always preview the task before submission – this way you can have a quick check of the specified parameters and also familiarize yourself with a “command line” way of doing bioinformatics.

Introduction to InsideDNA bioinformatics platform for tools & analysis Preview task screen

If you are satisfied with the task settings, you will need to select a Queue for the task. Different Queues provide different computing capacities (RAM in Gb and number of cores) and it is good idea to start with a smaller queue – for example, in our case it will be sufficient to either launch task with 4 cores and 15 Gb of RAM.

Introduction to InsideDNA bioinformatics platform for tools & analysis task queue screen

Once you selected a Queue, simply click on Submit task button. Once submitted, you can either go straight to the Task monitoring or Stay on the current page. Staying on the current Tools Settings is useful when you need to submit multiple similar tasks where you just modify input/output data and some parameters (aka “manual batch processing”). But for now click on View submitted task.

Introduction to InsideDNA bioinformatics platform for tools & analysis submitted task screen

8. Monitoring task progress

In Task bookmark you have several options:

1) Tasks are grouped by their status.

Introduction to InsideDNA bioinformatics platform for tools & analysis task groups view

Typically, an error-free task first appears in Running group and then automatically moves to Completed group. Sometimes, if you submit more than 5 tasks at once, extra tasks will be put on hold on (Pending group) – because right now you can run simultaneously 5 tasks.

Introduction to InsideDNA bioinformatics platform for tools & analysis pending task screen

Pending tasks will be launched as soon as one of the Running tasks is completed. If for some reasons your task went into Failed group, do not rush to restart it. After few minutes InsideDNA will automatically re-launch the task and will keep doing so until your task is successfully completed. So do not stress and give the platform few moments to help you out automatically.

2) You can always interact with submitted tasks by clicking on the buttons at the top menu. Same menu, but a dropdown will appear if you click on the arrow down button

Introduction to InsideDNA bioinformatics platform for tools & analysis buttons on top menu for inteaction

3) You can always preview your tasks for error log, Tool settings and general parameters such as type of queue at submission times.

Introduction to InsideDNA bioinformatics platform for tools & analysis error log screen

9. Obtaining the files

Now, let’s move to File Manager (FM). Click on Files and navigate into your root directory. Here you will see all files plus 2 extra folders with task_errors and task_logs.

Introduction to InsideDNA bioinformatics platform for tools & analysis file manager screen

 You can always preview what is inside of the file by clicking on the preview button on the right.

Introduction to InsideDNA bioinformatics platform for tools & analysis preview button in file manger

Plus many more operations typical for a normal file manager are available: copying./moving/delete/ rename/ files and folders, creating new folders, unarchiving, uploading and downloading files.

Introduction to InsideDNA bioinformatics platform for tools & analysis with other file manager option

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