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Networks are pervasive in society: infrastructures (e.g., telephone), commercial sectors (e.g., banking), and biological and genomic systems can be represented as networks. Consequently, there are software libraries that analyze networks. Containers (e.g., Docker, Singularity), which hold both runnable codes and their execution environments, are increasingly utilized by analysts to run codes in a platform-independent fashion. Portability is further enhanced by not only providing software library methods, but also the driver code (i.e., main() method) for each library method. In this way, a user only has to know the invocation for the main() method that is in the container. In this work, we describe an automated approach for generating a main() method for each software library method. A single intermediate representation (IR) format is used for all library methods, and one IR instance is populated for one library method by parsing its comments and method signature. An IR for the main() method is generated from that for the library method. A source code generator uses the main() method IR and a set of small, hand-generated source code templates|with variables in the templates that are automatically customized for a particular library method|to produce the source code main() method. We apply our approach to two widely used software libraries, SNAP and NetworkX, as exemplars, which combined have over 400 library methods.
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Single-particle chemical force microscopy to characterize virus surface chemistry
METHOD SUMMARY We developed a chemical force microscopy technique with a simple probe functionalization method using thiol attachment and an optimized covalent virus immobilization method. The novel method was used to detect the surface charge and hydrophobicity of viral capsids at a single-particle level.
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- Award ID(s):
- 1451959
- PAR ID:
- 10222318
- Date Published:
- Journal Name:
- BioTechniques
- Volume:
- 69
- Issue:
- 5
- ISSN:
- 0736-6205
- Page Range / eLocation ID:
- 363 to 370
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.2144/btn-2020-0085
