Highlighting SFA developer Mark Flynn of Los Alamos National Lab.
Oct 29, 2021

Community Highlight – Taxonomy Tools

The Los Alamos National Laboratory Bacterial-Fungal Science Focus Area team has developed a novel bioinformatics tool Genomic Origin Through Taxonomic Challenge (GOTTCHA2). The GOTTCHA2 App is a signature-based metagenomic taxonomic profiling method that combines high sensitivity to the presence of pathogens in a sample with low false negative rate. With GOTTCHA2 now available in KBase, more researchers can use this taxonomic profiler in combination with other tools, such as Kraken2 (in Beta). 

Mark Flynn, one of the software developers on the team, enjoys using the Jupyter notebook-like interface for constructing analysis pipelines within KBase. He recommends that KBase Users employ an app such as Trim Reads with Trimmomatic to remove low quality reads from their data, and then group their samples into a ReadsSet to facilitate taxonomic profiling of related reads.

KBase Developer Spotlight

Boris Sadkhin – Developer Training

Boris Sadkhin is a developer based at Argonne National Laboratory who runs Science Focus Area Developer training with the KBase Software Development Kit. Boris has supported SFA Developers with their App workflow planning and providing technical support and testing assistance. On this project, he supported the development of GOTTCHA2. 
What was exciting or challenging about this project?
(BS) It was great to see the progress they made. They were quick to learn the SDK and built out the apps and testing well.
What is your favorite kind of cookie? 
(BS) Medium chocolate chip 

Shane Canon – Project Lead

Please introduce yourself and tell users what you do at KBase.
(SC) As one of the KBase Leads, I’m responsible for overseeing much of the development of new features and capabilities in KBase. In addition to KBase, I’m also a lead for NMDC and am a staff member at the NERSC.
What was exciting or challenging about this project?
(SC) What I enjoy about working on KBase is developing a complex platform that can accelerate scientific discovery in biology. Guiding the development of software that can serve the diverse needs of this community and build towards the KBase vision is immensely challenging, but also very rewarding.
What is your favorite kind of cookie? 
(SC) I’m not sure I have a favorite cookie, but I enjoy a good bourbon.

Learn more

Watch the recorded Taxonomy Tools Webinar

For a quick, how-to, there is the GOTTCHA2 App Tutorial

Ellen Dow
Ellen Dow
Lawrence Berkeley National Laboratory

Ellen G. Dow, Ph.D. is a member of the outreach, communications, and user development team. Inspired by involvement in science outreach throughout graduate school, she left the bench to gain experience in informal education and cultivate community engagement from the general public to science sectors. A molecular biologist by training, Ellen applies her research experience to support scientists and develop resources for the KBase community.

appdev maintenance Feb 8

We will be performing maintenance on appdev.kbase.us on Wednesday, February 8, from 1pm-6pm CST (11am-4pm PST).  Parts of appdev will be unavailable during this time.

We do not anticipate any interruption to other KBase services.