In a genomics workflow, we’ll talk about Next Generation Sequencing (NGS) here, there are a lot of very similar steps. These steps pertain to some preparation such as histology and/or extraction, quantification, library preparation, sequencing and bioinformatics (pipeline, curation etc.). Although these steps are largely the same they come in many forms and use many different instruments and data.
Each of these areas of work can use many different instruments and data types but the basic input and output is the same. For example quantification can be done using PicoGreen, NanoDrop or Qubit on any number of plate reader instruments but the result is finding the concentration amount to direct downstream steps such as normalizing the sample concentration. Likewise, we may have many different index sets and use any number of robotic platforms to load them into a plate. A LIMS solution could be a basic framework of a web system to control workflow with hooks to plug in different modules. An example of a quantification & normalization by Qubit module:
Module: Quantification
- Hamilton liquid handler plate load protocol and plate setup screen to plug in to the LIMS
- LIMS interface to Synergy HX plate reader
- Resultant dilution calculations engine
Module: Normalization
- Hamilton liquid handler creates dilutions from results
- LIMS interface to take in new dilutions information
If we create a standard for developing these plugins we could open source the writing of such modules and share amongst the community.
See my collaboration idea here @ The Genomics Project
Software Development & Bioinformatics 