Posts in Software Development
Machine Learning Algorithms
Machine Learning Algorithms

A machine learning algorithm was developed that could reconstruct ab initio, the low resolution structure of a protein from its x-ray diffraction intensities alone.

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AI & Deep Learning, Algorithms, Modeling & Simulation, Software Development, ProjectGordon Webstermachine learning, genetic algorithms, molecular imaging, x-ray diffraction, structural biology, evolutionary algorithm, x-ray crystallography, protein structure, evolutionary computation
PyPop: Python For Population Genomics
PyPop: Python For Population Genomics

Amber Biology has been engaged to perform a full-scale overhaul of Python for Population Genomics (PyPop). PyPop is an open-source framework for large-scale population genomics. implemented to probe genotype data for signatures of natural selection.…

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Project, Genomics, Python, Software DevelopmentAlex Lancastergenome, genomics, genetics, genes, next-generation sequencing, sequencing, ngs, alleles, population genetics, pypop, hardy-weinberg
Blood Diagnostic Robot Software
Blood Diagnostic Robot Software

Amber Biology was hired to create sophisticated, custom machine control and user interface software for a medical diagnostic robot being developed by a team at Harvard Medical School

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Project, Python, Software DevelopmentGordon Webstersoftware, software development, programming, coding, computational biology, python, computation, computer science, programming language, robotics, robots, machine control, diagnostics, sepsis, infection, blood disease, hematology, antibodies
Data Mining To Optimize A Biological Manufacturing Process
Data Mining To Optimize A Biological Manufacturing Process

Algorithms were implemented in Python to correlate biomolecule manufacturing outcomes with process parameters, in order to improve the consistency and predictability of the manufacturing process…

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Project, Modeling & Simulation, Python, Software Development, Algorithms, AI & Deep Learning, Data ScienceJen Deadericksoftware, software development, programming, coding, computational biology, python, computation, computer science, programming language, big data, data science, data analysis, artificial intelligence, deep learning, genetic algorithms, AI, biomanufacturing, dna
Modeling A Drug's Mechanism of Action
Modeling A Drug's Mechanism of Action

A collaborative, cloud-based software platform being developed for modeling complex cell signaling pathways. This platform implemented a stochastic modeling approach underpinned by a rigorous semantic formalism that made possible a set of powerful static analyses of the modeled systems.

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Project, Algorithms, Modeling & Simulation, Software DevelopmentJen Deaderickcomputational biology, systems biology, bioinformatics, modeling, simulation, stochastic modeling, dynamic modeling, deterministic modeling, calculus, differential equations, complex adaptive systems, drug discovery, drug mechanism, pharmacology, drug development, user experience, ux, user experience design, ux design
Java-Based Platform For Immuno-Engineering Biotherapeutics
Java-Based Platform For Immuno-Engineering Biotherapeutics

A joint bioinformatics and laboratory-based program for predicting and re-engineering immunogenic regions in biologics that would eventually become a part of the standard workflow for all new biologic development programs throughout a global pharmaceutical company…

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Project, Algorithms, Software Development, ImmunologyJen Deaderickimmunology, immunogenicity, epitopes, T-cell epitopes, T-cell, immune response, antibody, antibodies, anaphylaxis, java, programming, software, software development, coding, computational biology, computation, computer science, programming language
Development Of An Agent-Based Toolkit For Modeling Complex Biological Systems
Development Of An Agent-Based Toolkit For Modeling Complex Biological Systems

Software development of Swarm, a pioneering open-source agent-based modeling toolkit from the Santa Fe Institute, and consulting with scientists using this toolkit to model complex biological systems such as transcription factor networks…

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Project, Algorithms, Modeling & Simulation, Software Development, PythonJen Deaderickcomputational biology, systems biology, bioinformatics, modeling, simulation, stochastic modeling, dynamic modeling, deterministic modeling, calculus, differential equations, complex adaptive systems, agent-based modeling
Cloud Computing Platform For Simulating Complex Cell-Signaling Networks
Cloud Computing Platform For Simulating Complex Cell-Signaling Networks

A commercial software-as-a-service (Saas) platform built on Amazon Web Services infrastructure, to allow biologists to collaboratively model and stimulate cell-signaling networks…

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Project, Modeling & Simulation, Software Development, Algorithms, Cloud ComputingJen Deaderickcomputational biology, systems biology, bioinformatics, modeling, simulation, stochastic modeling, dynamic modeling, deterministic modeling, calculus, differential equations, complex adaptive systems, cell signaling, cell signaling pathway, cell signaling network, cell biology, molecular biology, cloud computing
Workflow engine for large-scale sequence data
Workflow engine for large-scale sequence data

An Amber principal was involved in the development of the open-source COSMOS Python library for managing large-scale sequencing workflows.

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Project, Algorithms, Bioinformatics, Cloud Computing, Data Science, Python, Software DevelopmentAlex Lancastergenome, genomics, genetics, genes, next-generation sequencing, sequencing, ngs, alleles, population genetics, python, software, software development, programming, coding, computational biology