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Introducing Workflows in VLifeMDS

by V Ganesh on June 8th, 2012

Over an year ago we introduced scripting facility in VLifeMDS, allowing end-user customizations of VLifeMDS platform [see:]. Using scripting through Python, and over 70+ and growing functions provided by VLifeMDS platform, our customers have befitted immensely, especially when customization on the base platform were needed. One of the recent such instances was the  revamping of the IM-TECH Toxipred on-line server (, which uses VLifeMDS platform at the backend for a range of descriptor calculations.

Textual scripting, though providing absolute control over what you want to do with the VLifeMDS platform, is not intuitive for a large number of users who have less inclination towards programming. This set us out to develop an environment, within VLifeMDS platform, which would be GUI driven and more intuitive for a large section of users, and at the same time provide an easy interface for all the users to quickly customize and search for functionalities. One of the best ways to do this is use the concept of Workflows ( The scientific community at large have developed a number of generic workflow management systems (for instance KNIME, Project Trident). Most of these systems are available to use by the scientific community and one can easily use scripting interfaces provided with VLifeMDS to write plugins for these generic workflow management systems. Being generic, however, does not make these easily configurable for specific needs. To simplify these issues, we have build a new integrated, domain specific, workflow system for VLifeMDS platform, and is available to all the customers running version 4.2.x of the platform.This reminder of the post is intended to give a brief overview of how to use built-in workflows in VLifeMDS to simplify the way you work, typically when multi-stage processing is required.


A workflow example

Lets take an example of cleaning a PDB file. Cleaning a PDB file typically involves a number of steps, for simplicity lets narrow this down to only the following:

  1. Read in the PDB file
  2. Add hydrogens
  3. Retain only one or more chains
  4. Fix incomplete residues
  5. Complete missing residues
  6. Save the file (typically as .mol2) format

Performing the above activities using VLifeMDS standard GUI or for that matter other molecular modeling packages involve shuffling through a number of dialogs.  These are however repetitive activities and can be composed as a workflow, provided the above steps are packaged as workunits that can be connected by a user.

Simple PDB file cleaning workflow

Simple PDB file cleaning workflow

The above figure shows the same steps depicted as a workflow in VLifeMDS. Notice that the visual representation is much easier to comprehend at one shot and gives an overview of the activities happening to accomplish the whole process of PDB cleaning. Notice that the workunits above are colored depending on if the user is required to provide any additional parameters. A light orange color with thick red dotted lines indicates that there are user-editable parameters for this workunit that necessarily needs to be provided by the user for the execution to proceed. A white workunit indicates that there are no user-editable parameters for this workunit. Further a light green colored workunit indicates that there are user-editable parameters for this unit, but each of these parameters have some preset default values.


Domain specific language for workflows in VLifeMDS

Workflows in VLifeMDS uses a custom domain specific language rather than use a generic workflow management system. This allows for strict data type checking together with some extent of semantics checking when connecting the individual work units. It also allows for self-describing workunits that can be automatically connected without the user worrying about which inputs to connect to which outputs of the next workunit.


Search: its tags all the way

All workunits are tagged. When you build a workflow using these workunits, these are automatically tagged. Tags in VLifeMDS workflows are central to how you search and organize the workflows you have created. The user can add or remove tags as needed.


Overview of the interface

MDS Workflow interface
Click to Enlarge

The above image gives a glimpse of UI for workflows in VLifeMDS.


Quick video tour

 A quick video tool is available at Youtube:

There is more coming, visit us during the VLife user summit for a live demo at Hyatt Regency, Pune on 9th June 2012, 3pm onwards.


V Ganesh

I am software architect at VLife Sciences. I enjoy working with interfacing of science and technology. To know more about me drop in @ my personal blog:

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