benjamin.leopold.resume.json

resume.json

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  "basics": {
    "name": "Benjamin Leopold",
    "label": "Challenge seeker. Data wrangler. Communicator. Problem solver. Creative.",
    "email": "benjamin.leopold@cometsong.net",
    "phone": "860-992-5551",
    "location": {
      "city": "Farmington, CT",
      "countryCode": "USA"
    },
    "summary": "Combining interpersonal communication skills with 25+ years of biology and programming knowledge enables fluid collaboration with scientists, developers, stakeholders, and clients in the tasks designing, creating, and implementing innovative and effective new solutions used to move research and analysis projects forward.",
    "profiles": [
      {
        "network": "LinkedIn",
        "username": "linkedin.com/in/benjamin-leopold",
        "url": "https://linkedin.com/in/benjamin-leopold"
      },
      {
        "network": "GitHub",
        "username": "github.com/cometsong",
        "url": "https://github.com/cometsong"
      },
      {
        "network": "ORCID",
        "username": "0009-0000-4689-1126",
        "url": "https://orcid.org/0009-0000-4689-1126"
      }
    ]
  },
  "skills": [
    {
      "name": "Standards",
      "keywords": [ "OpenAPI", "JSON", "SQL", "GraphQL", "CommonMark", "Markdown", "HTML5", "CSS3", "XML", "TOML", "YAML", "UML", "ETCL" ]
    },
    {
      "name": "App frameworks",
      "keywords": [ "FastAPI", "Flask", "Django", "Ruby on Rails", "Drupal", "MediaWiki" ]
    },
    {
      "name": "SDLC Methodologies",
      "keywords": [ "Agile", "Scrum", "Kanban", "Waterfall", "BDD", "TDD" ]
    },
    {
      "name": "Languages",
      "keywords": [ "Python", "Bash", "Groovy", "Ruby", "JavaScript", "VisualBasic" ]
    },
    {
      "name": "Relational Databases",
      "keywords": [ "PostgreSQL", "MariaDB/MySQL", "SQLite", "Oracle" ]
    },
    {
      "name": "NoSQL Datastores",
      "keywords": [ "Redis", "memcached", "flatfiles" ]
    },
    {
      "name": "Workflow pipeline frameworks",
      "keywords": [ "Nextflow", "Cromwell", "WDL", "Ruffus", "Bash wrapper scripts" ]
    },
    {
      "name": "Testing / Linting",
      "keywords": [ "Pytest", "Unittest", "CI/CD", "Shellcheck", "Pylint", "Flake8" ]
    },
    {
      "name": "API Frameworks/Tools",
      "keywords": [ "Postman", "Swagger" ]
    },
    {
      "name": "Cluster",
      "keywords": [ "Slurm", "Torque PBS" ]
    },
    {
      "name": "Project Management / SCM",
      "keywords": [ "JIRA", "GitHub", "Confluence", "GitLab", "Git", "Mercurial", "Pre-Commit", "Semantic Versioning" ]
    },
    {
      "name": "Observation / Container / Visualization / Transition / Analytics",
      "keywords": [ "Datadog", "Kubernetes", "Singularity", "Docker", "KVM", "LucidChart", "LucidSpark", "NCBI data to SRA and GenBank", "Globus File Transfer", "CDMS and AER" ]
    }
  ],
  "work": [
    {
      "name": "GeneDx",
      "location": "Remote; Gaithersburg, MD",
      "url": "https://genedx.com",
      "startDate": "2021",
      "endDate": "2023",
      "position": "Senior Software Engineer",
      "description": "Genomics Interpretation Tool Engineering department",
      "highlights": [
        "Built modern, compelling, performant, high-quality applications for genetic counselors interacting with patients and for internal data miners at GeneDx.",
        "Designed and deployed projects for processing, analyzing, storing, and reviewing large-scale clinical genomic sequence data.",
        "Demonstrated experience in agile and incremental SDLC, covering planning, evaluation, design, development, testing, deployment, maintenance, and iteration. This encompasses backend server scripts, both new and existing ETL pipelines, APIs, microservices, full-stack web applications, both relational and non-relational databases (RDBMS, NoSQL), and reusable software libraries leveraging MVC patterns, all while adhering to clean coding standards.",
        "Rigorously and repeatedly tested software for functionality, performance, and security, employing automated CI/CD and local testing methodologies.",
        "Actively participated in team peer programming, PR reviews, and code reviews; providing support and mentorship junior team members.",
        "Collaborate closely with fellow engineers, product managers, and stakeholders.",
        "Led developers, documenters, and testers throughout the software development life cycle (SDLC)."
      ]
    },
    {
      "name": "The Jackson Laboratory for Genomic Medicine",
      "location": "Farmington, CT",
      "url": "https://jax.org",
      "startDate": "2013",
      "endDate": "2021",
      "position": "Bioinformatics Analyst",
      "description": "Microbial Genomics Core; Dr. Mark Adams group; Dr. George Weinstock group.",
      "highlights": [
        "Led and actively participated in the SDLC of custom software applications for the processing and analysis of large-scale clinical genomic data including WGS, mWGS, 16S, and RNASeq.",
        "Managed genomic sequence data for research groups by writing and maintaining ETL analysis pipelines, triaging raw data from sequencers through QC checks, and directing it to appropriate pipelines. Also handled data archival and deposition to public repositories (e.g., NCBI SRA).",
        "Designed and implemented web applications, one to track biological samples and corresponding sequencing libraries, and another for the modular display of sequencing runs and resulting FASTQ Q/C, as well as sample read counts.",
        "Developed and standardized data analysis pipelines and scripts and migrated between pipeline frameworks (e.g. Nextflow and Civet). Designed and created databases for storage research data and metadata.",
        "Managed sequence data for the NIH Integrated Human Microbiome Project (iHMP) research groups at Jackson Labs and Stanford. Aggregated, transformed, and consistently formatted (e.g., MIMARKS) a massive amount of sequence data and subject metadata. Collaborated with data managers from other nationwide research groups in the iHMP consortium to submit the data to the central repository.",
        "Determined methods for tracking epidemiological and genomic data associated with SARS CoV-2 variants as they were detected and moved throughout the New England area by working with a team to create an analysis and data presentation workflow."
      ],
      "high2": [
      ]
    },
    {
      "name": "University Hospital Münster",
      "location": "Münster, Germany",
      "url": "https://parodontologie.ukmuenster.de",
      "startDate": "2010",
      "endDate": "2013",
      "position": "Bioinformatician",
      "description": "Dr. Dag Harmsen group, Institute of Hygiene and Periodontology.",
      "highlights": [
        "Facilitated setup of a then state-of-the-art NGS sequencer (IonTorrent) for rapid sequencing of clinical microbial samples for research and diagnostic purposes. Installed software for data handling and analyses.",
        "Worked as part of a team of scientists to rapidly sequence samples, assemble reads, and characterize the European *E. coli* O104:H4 strain responsible for a large outbreak in 2011.",
        "Provided technology support to research groups by implementing and maintaining software for whole genome shotgun (WGS) sequencing, phylogenetic analyses, primer design, and for data storage and review."
      ]
    },
    {
      "name": "Jamin Webdesigns",
      "startDate": "2003",
      "endDate": "2010",
      "position": "Founder, Web Application and Site Developer",
      "highlights": [
        "Designed, programmed, and modified web applications and sites for charities and small businesses.",
        "Developed flagship product for all operational business data accessible, searchable, and publishable via web interface. Designed accompanying wiki documentation site."
      ]
    },
    {
      "name": "Leopold Photography",
      "location": "St. Louis, MO; Boston, MA; Puerto Rico; Guadalajara, Mexico; ...",
      "startDate": "2003",
      "endDate": "2010",
      "position": "Founder, Photographer, Digital Image Retoucher",
      "highlights": [
        "Editorial, architectural, product advertising, portrait, and musical performance photography.",
        "Retouched and processed images using Photoshop, Lightroom, Camera Raw, and Capture One.",
        "Lighting setup crew and digital handler on commercial and location photo shoots.",
        "Published in Billboard Radio Monitor, Boston Globe, St. Louis newspapers, websites, CD covers."
      ]
    },
    {
      "name": "Phase Forward",
      "location": "Waltham, MA",
      "startDate": "1998",
      "endDate": "2002",
      "position": "Technical Consultant; Senior Software Support Engineer",
      "highlights": [
        "Configured, implemented, and provided support for a clinical data management system (Clintrial) and a safety data tracking system (Clintrace). These applications served pharmaceutical companies, enabling them to record clinical study data, track adverse events, distribute data globally, catalog with coding dictionaries, and generate reports for government organizations such as the FDA. These products featured front-end GUIs interfacing with a backend Oracle database.",
        "Organized and conducted training classes for customers and consultants on the use and configuration of applications.",
        "Supervised a customer support group, overseeing the onboarding process for new hires on our product and database functionality."
      ]
    }
  ],
  "education": [
    {
      "institution": "Rochester Institute of Technology",
      "url": "https://www.rit.edu/",
      "area": "Biology",
      "studyType": "Bachelor of Science",
      "endDate": "1996"
    }
  ],
  "publications": [
    {
      "name": "Genome-based targeted sequencing as a reproducible microbial community profiling assay.",
      "publisher": "mSphere",
      "releaseDate": "2021",
      "url": "https://doi.org/10.1128/msphere.01325-20",
      "summary": "Benjamino J, **Leopold B**, Phillips D, Adams MD. With supplemental application https://github.com/TheJacksonLaboratory/MA-GenTA"
    },
    {
      "name": "Longitudinal multi-omics of host-microbial dynamics in prediabetes",
      "publisher": "Nature",
      "releaseDate": "2019",
      "url": "https://doi.org/10.1038/s41586-019-1236-x",
      "summary": "Zhou W*, Sailani MR*, Contrepois K*, Zhou Y*, Ahadi S*, [et al, including **Leopold B**] *(*co-first authors)*"
    },
    {
      "name": "The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease",
      "publisher": "Cell Host & Microbe",
      "releaseDate": "2014",
      "url": "https://doi.org/10.1016/j.chom.2014.08.014",
      "summary": "NIH Integrative HMP (iHMP) Research Network Consortium"
    },
    {
      "name": "Prospective genomic characterization of the German enterohemorrhagic *Escherichia coli* O104:H4 outbreak by rapid next generation sequencing technology",
      "publisher": "Journal: PloS One",
      "releaseDate": "2011",
      "url": "https://doi.org/10.1371/journal.pone.0022751",
      "summary": "Mellmann A*, Harmsen D*, Cummings CA*, [et al, including **Leopold B**] *(*co-first authors)*"
    }
  ],
  "languages": [
    {
      "language": "English",
      "fluency": "Native speaker"
    },
    {
      "language": "Spanish",
      "fluency": "Conversational"
    },
    {
      "language": "German",
      "fluency": "Lingering"
    }
  ],
  "interests": [
    {
      "name": "Poetry",
      "keywords": ["writing", "reading", "performing", "yawp!"]
    },
    {
      "name": "Bicycling",
      "keywords": ["road", "mountain", "bamboo"]
    },
    {
      "name": "Photography",
      "keywords": ["products", "headshots", "events", "concerts"]
    },
    {
      "name": "Theatre",
      "keywords": ["actor", "stage crew", "community"]
    },
    {
      "name": "Cooking",
      "keywords": ["breakfast", "lunch", "and", "dinner"]
    },
    {
      "name": "Kite Flying",
      "keywords": ["double", "triple"]
    },
    {
      "name": "Puzzles",
      "keywords": ["crossword", "jigsaw"]
    },
    {
      "name": "Gardening"
    },
    {
      "name": "Legos"
    }
  ],
  "projects": [
    {
      "name": "MA-GenTA",
      "description": "Targeted Probe Design Pipeline. Using mWGS genome bin clusters, prokka annotation predictions, and blast+ databases for generation, processing and filtering probe sequences.",
      "keywords": [ "bioinformatics", "pipeline", "annotation", "genome", "probe", "sequence", "microbiome", "ncbi-blast", "predictors", "targeted", "microbes" ],
      "url": "https://github.com/TheJacksonLaboratory/MA-GenTA",
      "roles": [ "Designer", "Developer" ],
      "type": "pipeline"
    },
    {
      "name": "Vim-CtrlSpace",
      "description": "Vim-CtrlSpace plug-in for managing your tabs, buffers, files, workspaces (sessions), bookmarks for your favorite projects, including fuzzy file search.",
      "keywords": [ "vim", "plugin", "organization" ],
      "url": "https://github.com/vim-ctrlspace",
      "roles": [ "Maintainer", "Contributor" ],
      "type": "plugin"
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