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Marc Schwering
Verified Expert in Engineering
Software Developer
Berlin, Germany
Toptal member since May 18, 2021
Bio
Marc is a software developer with a scientific background in molecular biotechnology and drug discovery and development. Since 2017, he has worked in a small DevOps team that supports the digital transition of R&D at Bayer Global. Marc has built IT solutions ranging from simple web apps to complex data warehouses. His combined scientific and development expertise and fluency in English, Chinese, French, and German bring great value to biotech and pharmaceutical companies.
Portfolio
docmetric GmbH
FastAPI, Elasticsearch, Cron, Python 3, Big Data, APIs, Back-end, ChatGPT API...
BCG GAMMA
React, PostgreSQL, FastAPI, Python 3, Docker, Docker Compose, MinIO, OAuth 2...
Bayer Global
Amazon Web Services (AWS), GitLab, Python 3, GraphQL, TypeScript, REST APIs...
Experience
- Python 3 - 7 years
- React - 4 years
- Amazon Web Services (AWS) - 4 years
- OAuth 2 - 4 years
- TypeScript - 3 years
- GitLab CI/CD - 3 years
- PyTorch - 3 years
- GraphQL - 2 years
Work Experience
Full-stack Developer
2023 - 2023
docmetric GmbH
- Created API endpoints for automatic statistical reporting.
- Wrote data pipelines for data enrichment and client exports.
- Reduced the runtime of a particular pipeline from weeks to hours through the relentless refactoring and exploiting of data structures.
- Identified artifacts and created filters to further stabilize pipelines and improve data quality based on regular anomaly analysis.
Technologies: FastAPI, Elasticsearch, Cron, Python 3, Big Data, APIs, Back-end, ChatGPT API, Databases, Web Servers, Gunicorn, Prompt Engineering, REST, DevOps, Linux
Software Developer
2022 - 2022
BCG GAMMA
- Developed CO2AI, a carbon accounting and simulating software for companies, as a full-stack developer with focus on the back end.
- Created an emission factors browser using good UX and NLP that helps users identify and remember relevant emission factors.
- Created a system for users to create and manage personal access tokens in an easy and secure way.
- Implemented an object storage proxy that can interface with AWS S3, Azure Blob, or a plain file system.
- Refactored existing systems for improving security and performance and reducing complexity.
Technologies: React, PostgreSQL, FastAPI, Python 3, Docker, Docker Compose, MinIO, OAuth 2, Keycloak, Pydantic, CircleCI, GitHub, NGINX, Node.js, APIs, Back-end, Databases, Web Servers, Gunicorn, Django, REST, DevOps, User Experience (UX), Linux, User Interface (UI)
Software Developer
2020 - 2021
Bayer Global
- Built a new serverless GxP-validated pharmacometrics IT landscape.
- Created fully validated and monitored computation environments for different statistical languages.
- Created automatic tracking of all data transformations a statistician could perform.
- Enabled efficient storage and browsing of data transformation graphs.
- Mentored colleagues in software development topics.
- Assisted HR with technical recruiting by creating developer tests and performing interviews.
Technologies: Amazon Web Services (AWS), GitLab, Python 3, GraphQL, TypeScript, REST APIs, React, GNU Multiple Precision (GMP), Python, Bash, HTML, HTML5, CSS, Serverless Framework, Serverless, Amazon Athena, Amazon EC2, Amazon RDS, DNS, AWS ELB, AWS ALB, GitLab CI/CD, OAuth 2, Ubuntu, Visual Studio Code (VS Code), PostgreSQL, Amazon DynamoDB, Translational Medicine, JavaScript, Docker, Docker Compose, Spark, AWS Serverless Application Model (SAM), Amazon API Gateway, AWS Lambda, Amazon S3 (AWS S3), Amazon Cognito, GxP, Amazon Aurora, Amazon Route 53, Science, Communication, CI/CD Pipelines, Node.js, APIs, Back-end, FastAPI, Databases, Web Servers, Gunicorn, Load Balancers, REST, DevOps, User Experience (UX), Linux, User Interface (UI)
Machine Learning Engineer
2020 - 2020
Bayer Global
- Created Antibody BERT, a transformer that can interpret antibody amino acid chains.
- Performed full pre-trainings of BERT on a large corpus of amino acid sequences.
- Performed further fine-tuning on several different downstream tasks.
- Researched current advances and pitfalls in NLP and BERTology.
- Assisted other researchers with deploying their machine learning models to a cloud infrastructure.
Technologies: PyTorch, PyTorch Lightning, NVIDIA CUDA, Natural Language Processing (NLP), Generative Pre-trained Transformers (GPT), BERT, Python 3, Optuna, Learning Transfer, Deep Learning, TensorBoard, Ray Tune, Python, Bash, Amazon EC2, Amazon Elastic Container Registry (ECR), DNS, AWS ELB, AWS ALB, GitLab CI/CD, Amazon Web Services (AWS), Ubuntu, Conda, Visual Studio Code (VS Code), GitLab, GitHub, REST APIs, PostgreSQL, Machine Learning, Translational Medicine, JavaScript, Plotly, Jupyter Notebook, Docker, Docker Compose, Amazon S3 (AWS S3), Computer Vision, Custom BERT, Distributed Learning, Amazon Route 53, Science, Communication, APIs, Back-end, FastAPI, Databases, Web Servers, Gunicorn, Load Balancers, REST, Linux
Software Developer
2017 - 2020
Bayer Global
- Created a data and metadata management and pipelining solution in the cloud.
- Developed and continuously improved two visual analytics platforms for the whole company.
- Assisted other colleagues with software development by mentoring and hosting learning sessions.
- Promoted product-focused and DevOps ways of working in the company.
Technologies: Amazon Web Services (AWS), GitLab, GitLab CI/CD, PyCharm, Visual Studio Code (VS Code), Python 3, JavaScript, TypeScript, React, D3.js, Chart.js, Plotly, PostgreSQL, REST APIs, GraphQL, Oracle, R, RStudio Shiny, RStudio, Jupyter Notebook, OAuth 2, SAML, LDAP, Java, Spring Boot, iRODS, Jenkins, Artifactory, Docker, Docker Compose, Docker Cloud, Docker Datacenter, Kubernetes, Spark, Hadoop, Python, Bash, HTML, HTML5, CSS, Flask, MySQL, Elasticsearch, Amazon EC2, Amazon Elastic Container Registry (ECR), Amazon RDS, DNS, AWS ELB, AWS ALB, Ubuntu, Amazon Elastic Container Service (ECS), Translational Medicine, Amazon Elastic MapReduce (EMR), Amazon API Gateway, AWS Lambda, Amazon S3 (AWS S3), Amazon Aurora, OpenAPI, Canvas, NGINX, Amazon Route 53, Science, Communication, CI/CD Pipelines, Node.js, APIs, Back-end, FastAPI, Databases, Web Servers, Gunicorn, Load Balancers, Django, REST, DevOps, User Experience (UX), Linux, User Interface (UI), Neo4j
Student Researcher
2015 - 2017
German Cancer Research Center
- Performed cell assays linking the Hippo pathway with HIPK2.
- Developed a machine learning model to predict enigm mRNA-binding proteins.
- Performed pooled CRISPR/Cas9 screens to study the Wnt signaling pathway.
- Created the CRISPRAnalyzeR app to easily analyze data from CRISPR/Cas9 screens.
- Completed my MSc thesis on characterizing batch effects in scRNA sequencing experiments.
Technologies: Single-cell RNA Sequencing, scRNA-seq, Differential Expression Analysis, Batch Effects, CRISPR/Cas9, Pooled CRISPR/Cas Screening, FACS, Mathematical Modeling, Machine Learning, Shrinkage Discriminant Analysis (SDA), Multivariate Adaptive Regression Splines (MARS), Biochemical Assays, Genetic Engineering, Cellular Assays, R, RStudio Shiny, CRISPR/Cas, GitLab, Python 3, PostgreSQL, Ubuntu, Bash, MySQL, XGBoost, REST APIs, scRNA-seq Analysis, Genome-wide RNA-seq Analysis, Translational Medicine, Biology, Spatio-temporal Modeling and Simulation, Highcharts, RStudio, Docker, Pooled CRISPR/Cas Screen Analysis, qPCR, Single cell RNA Sequencing Analysis, Science, Communication, Python, HTML5, HTML, CSS, Databases, Web Servers, Linux
Student Researcher
2015 - 2015
Max Planck Institute for Intelligent Systems
- Designed and built microfluidic devices for microdroplet experiments.
- Characterized surfactant mixtures using traditional methods, such as sessile drop.
- Set up and performed experiments to characterize microdroplets directly inside microfluidic devices.
- Used droplet deformation characteristics to infer physical properties.
- Developed an app to automatically analyze image data and return the physical properties of microdroplets.
Technologies: Microdroplet Microfluidics, Lithography, Biomimetic Systems, Computer Vision, GitLab, Python 3, PostgreSQL, Ubuntu, Bash, Mathematical Modeling, Genetic Engineering, Spatio-temporal Modeling and Simulation, R, RStudio, mRNA Extraction, Droplets, Digital Imaging, Science, Databases
Student Intern Abroad
2013 - 2014
Acumen Research Laboratories
- Performed leukocyte mRNA extraction and qPCR on call for a POC study.
- Assisted with setting up a procurement platform for a Singaporean research consortium.
- Played a key role in finding investors at MEDICA, the world's largest medical trade fair.
Technologies: mRNA Extraction, Leukocyte mRNA Extraction, qPCR, Bash, Translational Medicine, Biology, Science, Communication, Databases
Student Intern Abroad
2010 - 2010
Mycenax Biotech
- Tested dynamic binding capacities of different materials to optimize downstream procedures.
- Assisted with taking and analyzing samples for quality control in a GMP laboratory.
- Assisted with general quality assurance activities.
Technologies: GNU Multiple Precision (GMP), Quality Control (QC), Quality Assurance (QA), Bash, Genetic Engineering, Biology, Science, Databases
Project History
MagicSoup: A Cellular Evolution Game
https://magic-soup.readthedocs.io/I created a game that simulates cell metabolic and transduction pathway evolution. With user-defined chemistry, cells can evolve proteins with different domains and kinetic properties. They thereby create complex signal processing networks. As is the case in nature, these networks consist of structures such as hubs, feedback loops, and oscillators from which complex behavior emerges. I implemented the simulation as a Python package, with most calculations being done in CUDA kernels.
CO2AI: AI for Sustainability
As part of a team at BCG GAMMA, I developed CO2AI, an app to reduce carbon emissions. CO2AI is a carbon accounting and simulation platform for companies. It integrates large, curated libraries of emission factors to create accurate and detailed predictions based on simulations and business forecasts.
As of now, it is the most widely used and feature-rich carbon accounting app on the market. As a full-stack developer, I created several new features and helped in refactoring, increasing performance, and security.
As of now, it is the most widely used and feature-rich carbon accounting app on the market. As a full-stack developer, I created several new features and helped in refactoring, increasing performance, and security.
Android App: Ankerwache
https://github.com/mRcSchwering/ankerwacheAn anchor watch app I built for Android using React Native and Expo. The app is designed to help users sleep better while on a boat at anchor. A user sets their anchor position, defines a radius, and starts the anchor watch. If their phone is persistently outside the defined radius, it will ring loudly.
Prevailing Winds App
https://www.prevailing-winds.de/I developed this as a weekend side project. It's an interactive pilot chart for surfers, pilots, sailors, paragliders, and anyone interested in wind strength and directions. Many great apps, like Windy.com, show you the current winds with short-term predictions. However, I didn't find anything with historical wind data. Prevailing Winds is an excellent tool for planning holidays or a passage.
Pharmacometrics IT Landscape
I built a GxP-validated pharmacometrics IT landscape as part of a DevOps team. The old one had to be replaced, and, instead of just re-creating all its parts, we wanted to design it to be more efficient and flexible. Thus, apart from developing the landscape itself, time was spent understanding users, business processes, and regulatory requirements.
Antibody BERT
In a machine learning research group, I created a transformer that predicts antibody characteristics. I redesigned a BERT—a transformer commonly used in NLP—to understand amino acid chains of antibodies. Then, I pre-trained this transformer on hundreds of millions of antibodies and fine-tuned it to specific problems in the drug discovery and development pipeline.
Digital Beehive
https://github.com/bayer-science-for-a-better-life/beehiveThis was a small side project I did to help beekeepers. I developed and trained a model that can detect the content of a honeycomb photo; for example, it can count the number of cells within larvae, pollen, and nectar. You can use this to get an accurate estimate of your beehive's health.
Visual Analytics Platforms
As part of the DevOps team, I developed, deployed, and maintained two visual analytics platforms, one for genes and one for diseases. These platforms combined multiple data sources of each entity and represented them in interactive plots. One exciting aspect of this project was to find clear, useful, and scientifically accurate ways of representing the data. Another interesting aspect was the harmonization of data and curation of ontologies.
Biotop Community Lab e.V.
I co-founded and supported Biotop Community Lab e.V. and served as vice-chairman. This is a no-profit organization for promoting the democratization of science through access to biotechnology and learn-by-doing education. We are a part of the global DIY-bio movement, which focuses on bringing biology outside of academic and industrial environments to the lay public. We believe that biology is technology, and we want to put citizens in conditions to make use of it like any other common technology.
CRISPR-AnalyzeR
A web app I wrote during my master's degree program when working with pooled CRISPR/Cas9 screens. Analyzing the data from these screens is tedious and largely repetitive. This tool does all the pre-processing, data quality checks, and differential distribution calculations. Years later, I noticed this tool was used by several pharma companies.
Synthetic Cells in Microdroplets
I worked in a microfluidics laboratory that wanted to create synthetic cells using microdroplet technology. To do this, surfactant mixtures had to be optimized. I assisted in establishing a system that could measure surface tension and other physical properties directly inside the microdroplets using computer vision.
Sepsis Diagnostic Genetic Assay
A Singaporean startup found a set of genes that were differentially expressed in leukocytes of sepsis patients. I facilitated a proof of value study by analyzing patient blood samples on call. The work included leukocyte mRNA extraction and qPCR.
Batch Effects in Single Cell RNA Sequencing Analysis
This was my MSc thesis. Data from single cell RNA sequencing experiments are often confounded with technical variability due to experimental batches. Using mathematical modeling and machine learning methods, I measured these batch effects and predicted significant differential distributions.
In Vivo and in Silico Creation of a Static Min System in E. Coli
This was my BSc thesis. It combined spatial simulations and synthetic biology to compare static and spatio-temporal oscillating concentration gradients within the cell. The work included modeling experiments in silico and then performing them in vivo.
Education
2013 - 2017
Master of Science in Molecular Biotechnology
University of Heidelberg - Heidelberg, Germany
2010 - 2013
Bachelor of Science Degree in Molecular Biotechnology
University of Heidelberg - Heidelberg, Germany
Skills
Libraries/APIs
React, PyTorch, PyTorch Lightning, REST APIs, Node.js, GNU Multiple Precision (GMP), Ray Tune, D3.js, Chart.js, Leaflet, OpenAPI, XGBoost, Highcharts, SQLAlchemy, Pydantic
Tools
GitLab, GitLab CI/CD, Docker Compose, GitHub, Amazon Elastic Container Service (ECS), AWS ELB, TensorBoard, PyCharm, Plotly, Jenkins, Artifactory, Amazon Elastic MapReduce (EMR), Amazon Cognito, Canvas, NGINX, Amazon Athena, Amazon Elastic Container Registry (ECR), Expo, Celery, Keycloak, CircleCI, PyPI, Cron
Languages
Python 3, TypeScript, Python, Bash, GraphQL, JavaScript, R, HTML, HTML5, CSS, SAML, Java, TypeScript 3, Rust
Paradigms
REST, DevOps
Platforms
Ubuntu, Amazon Web Services (AWS), Docker, RStudio, AWS Lambda, AWS ALB, Amazon EC2, Visual Studio Code (VS Code), Linux, NVIDIA CUDA, Oracle, Jupyter Notebook, Docker Datacenter, Kubernetes, Droplets, Android
Storage
Amazon S3 (AWS S3), PostgreSQL, Amazon DynamoDB, Amazon Aurora, MySQL, Databases, Docker Cloud, Elasticsearch, Redis, Neo4j
Frameworks
OAuth 2, RStudio Shiny, Flask, Serverless Framework, Optuna, Spring Boot, Spark, Hadoop, AWS Serverless Application Model (SAM), React Native, Alembic, JSON Web Tokens (JWT), Django
Other
BERT, Conda, Machine Learning, Biology, Deep Learning, Amazon API Gateway, Shrinkage Discriminant Analysis (SDA), Multivariate Adaptive Regression Splines (MARS), Custom BERT, mRNA Extraction, Single cell RNA Sequencing Analysis, Science, Communication, Serverless, Amazon RDS, FastAPI, APIs, Back-end, Machine Learning Operations (MLOps), Web Servers, Gunicorn, User Experience (UX), User Interface (UI), Mathematical Modeling, scRNA-seq Analysis, Genome-wide RNA-seq Analysis, Microdroplet Microfluidics, Genetic Engineering, Cellular Assays, Biochemical Assays, Pooled CRISPR/Cas Screening, Lithography, Translational Medicine, Biomimetic Systems, Entrepreneurship, Spatio-temporal Modeling and Simulation, Neurobiology, Natural Language Processing (NLP), Learning Transfer, LDAP, iRODS, Cloudflare, Geography, Single-cell RNA Sequencing, scRNA-seq, Differential Expression Analysis, Batch Effects, CRISPR/Cas9, FACS, Computer Vision, CRISPR/Cas, Pooled CRISPR/Cas Screen Analysis, GxP, Distributed Learning, Amazon Route 53, Leukocyte mRNA Extraction, qPCR, Quality Control (QC), Quality Assurance (QA), Digital Imaging, Physics Simulations, DNS, GitHub Actions, Geolocation, CI/CD Pipelines, MinIO, Biotechnology, Multiprocessing, Chemistry, Packaging, Simulations, Networks, Generative Pre-trained Transformers (GPT), Big Data, Hugging Face, Large Language Models (LLMs), ChatGPT API, Prompt Engineering, Load Balancers
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