John M. Fonner

Biocompatibility Implications of Polypyrrole Synthesis Techniques

Polypyrrole (PPy) is an inherently conducting polymer that has shown great promise for biomedical applications within the nervous system. However, to effectively use PPy as a biomaterial implant, it is important to understand and reproducibly control the electrical properties, physical topography and surface chemistry of the polymer. Although there is much research published on the use of PPy in various applications, there is no systematic study linking the methodologies used for PPy synthesis to PPys basic polymeric properties (e.g., hydrophilicity, surface roughness), and to the biological effects these properties have on cells. Electrochemically synthesized PPy films differ greatly in their characteristics depending on synthesis parameters such as dopant, substrate and thickness, among other parameters. In these studies, we have used three dopants (chloride (Cl), tosylate (ToS), polystyrene sulfonate (PSS)), two substrates (gold and indium tin oxide-coated glass), and a range of thicknesses, to measure and compare the biomedically important characteristics of surface roughness, contact angle, conductivity, dopant stability and cell adhesion (using PC-12 cells and Schwann cells). As predicted, we discovered large differences in roughness depending on the dopant used and the thickness of the film, while substrate choice had little effect. From contact angle measurements, PSS was found to yield the most hydrophilic material, most likely because of free charges from the long PSS chains exposed on the surface of the PPy. ToS-doped PPy films were tenfold more conductive than Cl- or PSS-doped films. X-ray photoelectron spectroscopy studies were used to evaluate dopant concentrations of PPy films stored in water and phosphate buffered saline over 14 days, and conductance studies over the same timeframe measured electrical stability. PSS proved to be the most stable dopant, though all films experienced significant decay in conductivity and dopant concentration. Cell adhesion studies demonstrated the dependence of cell outcome on film thickness and dopant choice. The strengths and weaknesses of different synthesis parameters, as demonstrated by these experiments, are critical design factors that must be leveraged when designing biomedical implants. The results of these studies should provide practical insight to researchers working with conducting polymers, and particularly PPy, on the relationships between synthesis parameters, polymeric properties and biological compatibility.

Identification of a Novel Inhibitor of Dengue Virus Protease through Use of a Virtual Screening Drug Discovery Web Portal

We report the discovery of a novel small-molecule inhibitor of the dengue virus (DENV) protease (NS2B-NS3pro) using a newly constructed Web-based portal (DrugDiscovery@TACC) for structure-based virtual screening. Our drug discovery portal, an extension of virtual screening studies performed using IBMs World Community Grid, facilitated access to supercomputer resources managed by the Texas Advanced Computing Center (TACC) and enabled druglike commercially available small-molecule libraries to be rapidly screened against several high-resolution DENV NS2B-NS3pro crystallographic structures. Detailed analysis of virtual screening docking scores and hydrogen-bonding interactions between each docked ligand and the NS2B-NS3pro Ser135 side chain were used to select molecules for experimental validation. Compounds were ordered from established chemical companies, and compounds with established aqueous solubility were tested for their ability to inhibit DENV NS2B-NS3pro cleavage of a model substrate in kinetic studies. As a proof-of-concept, we validated a small-molecule dihydronaphthalenone hit as a single-digit-micromolar mixed noncompetitive inhibitor of the DENV protease. Since the dihydronaphthalenone was predicted to interact with NS2B-NS3pro residues that are largely conserved between DENV and the related West Nile virus (WNV), we tested this inhibitor against WNV NS2B-NS3pro and observed a similar mixed noncompetitive inhibition mechanism. However, the inhibition constants were ∼10-fold larger against the WNV protease relative to the DENV protease. This novel validated lead had no chemical features or pharmacophores associated with adverse toxicity, carcinogenicity, or mutagenicity risks and thus is attractive for additional characterization and optimization.

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements

BackgroundThe genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they are somatically generated in each developing lymphocyte by a process called V(D)J recombination, which assembles specific, independent gene segments into mature composite genes. The full set of composite genes in an individual at a single point in time is referred to as the immune repertoire. V(D)J recombination is the distinguishing feature of adaptive immunity and enables effective immune responses against an essentially infinite array of antigens. Characterization of immune repertoires is critical in both basic research and clinical contexts. Recent technological advances in repertoire profiling via high-throughput sequencing have resulted in an explosion of research activity in the field. This has been accompanied by a proliferation of software tools for analysis of repertoire sequencing data. Despite the widespread use of immune repertoire profiling and analysis software, there is currently no standardized format for output files from V(D)J analysis. Researchers utilize software such as IgBLAST and IMGT/High V-QUEST to perform V(D)J analysis and infer the structure of germline rearrangements. However, each of these software tools produces results in a different file format, and can annotate the same result using different labels. These differences make it challenging for users to perform additional downstream analyses.ResultsTo help address this problem, we propose a standardized file format for representing V(D)J analysis results. The proposed format, VDJML, provides a common standardized format for different V(D)J analysis applications to facilitate downstream processing of the results in an application-agnostic manner. The VDJML file format specification is accompanied by a support library, written in C++ and Python, for reading and writing the VDJML file format.ConclusionsThe VDJML suite will allow users to streamline their V(D)J analysis and facilitate the sharing of scientific knowledge within the community. The VDJML suite and documentation are available from https://vdjserver.org/vdjml/. We welcome participation from the community in developing the file format standard, as well as code contributions.

Launcher: A Shell-based Framework for Rapid Development of Parallel Parametric Studies

Petascale computing systems have enabled tremendous advances for traditional simulation and modeling algorithms that are built around parallel execution. Unfortunately, scientific domains using data-oriented or high-throughput paradigms have difficulty taking full advantage of these resources without custom software development. This paper describes our solution for rapidly developing parallel parametric studies using sequential or threaded tasks: The launcher. We detail how to get ensembles executing quickly through common job schedulers SGE and SLURM, and the various user-customizable options that the launcher provides. We illustrate the efficiency of or tool by presenting execution results at large scale (over 65,000 cores) for varying workloads, including a virtual screening workload with indeterminate runtimes using the drug docking software Autodock Vina.

VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements

Background Recent technological advances in immune repertoire sequencing have created tremendous potential for advancing our understanding of adaptive immune response dynamics in various states of health and disease. Immune repertoire sequencing produces large, highly complex data sets, however, which require specialized methods and software tools for their effective analysis and interpretation. Results VDJServer is a cloud-based analysis portal for immune repertoire sequence data that provide access to a suite of tools for a complete analysis workflow, including modules for preprocessing and quality control of sequence reads, V(D)J gene segment assignment, repertoire characterization, and repertoire comparison. VDJServer also provides sophisticated visualizations for exploratory analysis. It is accessible through a standard web browser via a graphical user interface designed for use by immunologists, clinicians, and bioinformatics researchers. VDJServer provides a data commons for public sharing of repertoire sequencing data, as well as private sharing of data between users. We describe the main functionality and architecture of VDJServer and demonstrate its capabilities with use cases from cancer immunology and autoimmunity. Conclusion VDJServer provides a complete analysis suite for human and mouse T-cell and B-cell receptor repertoire sequencing data. The combination of its user-friendly interface and high-performance computing allows large immune repertoire sequencing projects to be analyzed with no programming or software installation required. VDJServer is a web-accessible cloud platform that provides access through a graphical user interface to a data management infrastructure, a collection of analysis tools covering all steps in an analysis, and an infrastructure for sharing data along with workflows, results, and computational provenance. VDJServer is a free, publicly available, and open-source licensed resource.

VDJPipe: A pipelined tool for pre-processing immune repertoire sequencing data

BackgroundPre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input for downstream analysis. VDJPipe is a flexible, high-performance tool that can perform multiple pre-processing tasks with just a single pass over the data files.ResultsProcessing tasks provided by VDJPipe include base composition statistics calculation, read quality statistics calculation, quality filtering, homopolymer filtering, length and nucleotide filtering, paired-read merging, barcode demultiplexing, 5′ and 3′ PCR primer matching, and duplicate reads collapsing. VDJPipe utilizes a pipeline approach whereby multiple processing steps are performed in a sequential workflow, with the output of each step passed as input to the next step automatically. The workflow is flexible enough to handle the complex barcoding schemes used in many immunosequencing experiments. Because VDJPipe is designed for computational efficiency, we evaluated this by comparing execution times with those of pRESTO, a widely-used pre-processing tool for immune repertoire sequencing data. We found that VDJPipe requires <10% of the run time required by pRESTO.ConclusionsVDJPipe is a high-performance tool that is optimized for pre-processing large immune repertoire sequencing data sets.

Launcher: A simple tool for executing high throughput computing workloads

Launcher (Wilson and Fonner 2014, Wilson (2016), Wilson (2017)) is a utility for performing simple, data parallel, high throughput computing (HTC) workflows on clusters, massively parallel processor (MPP) systems, workgroups of computers, and personal machines. It can be easily run from userspace or installed for system-wide use on shared resources. Launcher will perform automatic process binding on multi-/many-core architectures where hwloc (“Portable Hardware Locality (Hwloc)” n.d.) is installed.

The Agave Platform: An Open, Science-as-a-Service Platform for Digital Science

The Agave Platform first appeared in 2011 as a pilot project for the iPlant Collaborative [11]. In its first two years, Foundation saw over 40% growth per month, supporting 1000+ clients, 600+ applications, 4 HPC systems at 3 centers across the US. It also gained users outside of plant biology. To better serve the needs of the general open science community, we rewrote Foundation as a scalable, cloud native application and named it the Agave Platform. In this paper we present the Agave Platform, a Science-as-a-Service (ScaaS) platform for reproducible science. We provide a brief history and technical overview of the project, and highlight three case studies leveraging the platform to create synergistic value for their users.