Senior Design Projects
ECS193 A/B Winter & Spring 2022
Automated quality control and assurance of stable isotope measurements
| ********** | |
| Name | Chris Yarnes |
| Affiliation | UC Davis Stable Isotope Facilty |
Project's details
| Project title | Automated quality control and assurance of stable isotope measurements |
| Background | Stable isotopes of elements are naturally occurring variants in atomic weight that are influenced by a host of biogeochemical processes – everything from enzymatics to evaporation to photochemistry – making their measurements extremely useful to a range of “environmental forensics”. The UC Davis Stable Isotope Facility provides analytical services for a range of stable isotope applications, including paleoclimatology, fraud in the pharmaceutical and food industries, forensics of improvised explosives, marine food web reconstruction, identifying sources of greenhouse gases, and human nutrition, among others. Because stable isotopes are sufficiently rare and cannot routinely be measured directly at the atomic level, a host of quality control and assurance procedures are necessary to ensure scientifically reproducible measurements. |
| Description | The quality control and assurance of stable isotope measurements can become cumbersome when applied to measurements of an array of compounds from a single sample source, such as individual amino acids from human hair (compound-specific stable isotope analysis; “CSIA”). This requires a complex, conditional series of data manipulations following instrumental analysis in order to achieve a calibrated, archive-quality data set. Several years ago, the UCD Stable Isotope Facility helped to design a Python software package for CSIA quality assurance procedures, but the design was limited in scope to a single measurement type. Despite its limitations and lack of official distribution, a number of other laboratories have adopted this software, including the University of Alaska, Louisiana State University, and the National Oceanic Atmospheric Administration. We are certain that a more generalizable software package for CSIA quality assurance would be quickly adopted across the broader scientific community. |
| Deliverable | Following consultation with UCD Stable Isotope Facility scientists regarding the required analytical processes and tools for the software, the design team will review the code and GUI of the existing software and decide whether to (1) upgrade the present code and GUI with additional and more generalizable functionality or (2) to initiate a new design that provides the full suite of analytical tools. The goal is for a flexible design that allows for customizable ingest templates and would be suitable for a range of applications with differing needs for quality control and assurances procedures. Ideally, the design will also include export functionality to interface with ISOBANK, an NSF-funded open global repository of stable isotope measurements (http://www.isobank.org). |
| Skill set desirable | We are hoping for a team with the desire and ability to bring fresh design perspectives to this project. While not necessarily within the scope of the proposed project, it is our long-term goal to make such a software package freely available (e.g. GitHub). Direct and full attribution will be made to the design team’s contribution upon any release. As the package will be primarily used by scientists, the program will ideally be constructed with Python or R. |
| Phone number | ********** |
| Client time availability | 30-60 min weekly or more |
| IP requirement | Open source project |
| Attachment | Click here |
| Selected | No |
| Team members | N/A |
| TA | N/A |