Scientific Software Development
Bioinformatics and LIMS Solutions
Off the shelf or open source, the best scientific
informatics solutions integrate it all...
seamlessly
Off the shelf or open source, the best scientific
informatics solutions integrate it all...
seamlessly
This tool is capable of integrating genomic data from many sources. Data sources may be internal to your organization or public datasources. The GWAS track in this demo is a unique way to view the rapidly growing GWAS catalog. The backend server is Tomcat, running a Java Jersey Web Service framework in a Maven Project.
The organization's public data of interest is either loaded into MongoDB with PyMongo Python scripts for operational big data or compiled into indexed Tabix based files like BigBed. Most any genomic data can be compiled into Tabix, BigWig, or BigBed files for viewing in genome browsers.
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In this example, we integrate the Bioconductor - ChemmineR package to cluster on structure similarity of top screening hits.
The scatterplot uses R Plotly to visualize assay activity score and molecular weight simultaneously.
For both R shiny apps, data is read from a dynamic web service.
Getting an open source R package to run in your environment is rarely easy. With Docker, you only have to do it once.
This tools demonstrates a chemical structure registry and search platform that is powerful but doesn't include lots of licensing costs. The backend server is Tomcat, running a Java Jersey Web Service framework in a Maven Project. The structure database is Postgres, and Bingo from EPAM. The server also uses the powerful EPAM Indigo Java API.
The demo shows good performance on just a micro server instance. It also shows how it can be well integrated with other datasources like the Pubchem RESTful API.
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The example LIMS pictured is a custom Java Web Start application that communicates with Pipeline Pilot web services. It organizes plates, racks, tubes and vials into workgroups.
Workgroups have workflows that can be updated manually or robotically. Material requests, plate and rack manipulations and dozens of reports were also integrated.
These demos are kept very lightweight to keep our AWS costs down. They are example designs that can, or have been, scaled up into larger solutions. They leverage cloud computing and various open source tools.
We plan to continue adding examples. Contact us if you want to know more or have a pharmaceutical / biotech software informatics contract project need in the Greater Boston / Cambridge area.
The opensource Biodalliance browser was plugged into the client side javascript code. Enhancements were made to the browser code. Any or all of the features can be clicked and the data with the track can be sent to a table below the browser for export.
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This lightweight demo is actually running from two docker containers on an AWS EC2 instance. One container for Tomcat and one for Mongodb. Version control is GIT.
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The opensource JSME sketcher was plugged into the client side javascript code. Registration looks up a pubchem structure and adds it to the local Bingo registry if the exact compound is not already registered
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This lightweight demo is actually running from three docker containers on an AWS EC2 instance. One container for Tomcat, postgres and R Shiny. Version control is GIT.
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