Sofiene Khiari

Sofiene Khiari

Pharmacist & Software Developer

I'm a driven pharmacist currently pursuing a PhD in the Computational Pharmacy Group at the University of Basel, where I blend my passion for Pharmaceutical Sciences and Computer Sciences to push the boundaries of what's possible in drug discovery.

As a staunch advocate of Open Source Software and Open Science, I'm committed to contributing to the community and fostering a spirit of collaboration. I believe that the future of pharmaceutical innovation lies at the intersection of cutting-edge computational methods and traditional pharmaceutical expertise — a space where I thrive.

Driven by a desire to make a tangible difference, I strive to develop groundbreaking pharmaceutical technologies that don't just advance the science, but do so with a keen focus on R&D costs and accessibility. My work is guided by a simple yet powerful principle: transformative solutions should be within reach for those who need them most.

Whether you're interested in collaboration, innovation, or exploring how computational approaches can revolutionize pharmaceutical research, I'd love to connect.

Experience

$ git log --oneline --graph --all

Changes not yet committed:

(working) build: Obtain Doctor of Philosophy diploma

······· build: Obtain Doctor of Philosophy diploma
8b2e4f1 build: Obtain MSc Drug Sciences diploma
5c9a3d2 build: Obtain Pharmaciae Doctor diploma
7f1b8e3 feat: Complete internship at Bone Marrow Transplantation Center
2d6c4a9 feat: Complete internship at local pharmacy
9e3f7b1 feat: Complete internship at Saïd pharmaceutical industry
4a8d2c6 spike: Complete training at Mongi-Slim Hospital
1b5e9f4 spike: Complete training at local pharmacy
3f7b2e5 init: Obtain Baccalauréat diploma

build: Obtain Doctor of Philosophy diploma

status: working (uncommitted)
started: January 2025
Author: Sofiene Khiari <research@sofk.ch>

University of Basel, Switzerland — Computational Pharmacy Group

Developing LLM-based Agentic AI systems for researchers working in computer-based drug design to help with decision making in lead selection, under the supervision of Prof. Markus A. Lill.

build: Obtain MSc Drug Sciences diploma

commit 8b2e4f1
Date: September 2021 — December 2024
Author: Sofiene Khiari <research@sofk.ch>

University of Basel, Switzerland

Master of Science in Drug Sciences. Field: Pharmaceutical Sciences. Conferred by the Faculty of Science, 12 December 2024.

build: Obtain Pharmaciae Doctor diploma

commit 5c9a3d2
Date: September 2010 — February 2019
Author: Sofiene Khiari <research@sofk.ch>

University of Monastir, Tunisia

Field: Pharmacy. Minor: Industrial Pharmacy. Degree: Pharmaciae Doctor.

Thesis (September 2018 — February 2019): "Comparison between two disinfectants used in the production of cytotoxic drugs in a cytotoxic safety station."

feat: Complete internship at Bone Marrow Transplantation Center

commit 7f1b8e3
Date: March 2018 — August 2018
Author: Sofiene Khiari <research@sofk.ch>

National Center for Bone Marrow Transplantation, Tunisia

Management of drugs and medical products, pharmaceutical analysis and validation of prescriptions, securing the drug circuit, prevention of drug iatrogenesis, therapeutic education, preparation of cancer drugs (magistral preparations), pharmacovigilance and material monitoring, and clinical studies.

feat: Complete internship at local pharmacy

commit 2d6c4a9
Date: December 2017 — February 2018
Author: Sofiene Khiari <research@sofk.ch>

Local pharmacy, Tunisia

Medication dispensing and patient counselling.

feat: Complete internship at Saïd pharmaceutical industry

commit 9e3f7b1
Date: September 2017 — November 2017
Author: Sofiene Khiari <research@sofk.ch>

Saïd pharmaceutical industry, Tunisia

Overview of the work basics in all departments of the pharmaceutical industry. Creation of an Excel matrix to optimize the evaluation of elementary impurities during the production of medicines according to the guideline ICH Q3D STEP 4.

spike: Complete training at Mongi-Slim Hospital

commit 4a8d2c6
Date: August 2016
Author: Sofiene Khiari <research@sofk.ch>

Mongi-Slim Hospital, Marsa, Tunisia

Overview of nursing work in a clinical anaesthesia department.

spike: Complete training at local pharmacy

commit 1b5e9f4
Date: August 2013
Author: Sofiene Khiari <research@sofk.ch>

Local pharmacy, Tunisia

Overview of the work in a local pharmacy.

init: Obtain Baccalauréat diploma

commit 3f7b2e5
Date: September 2006 — July 2010
Author: Sofiene Khiari <research@sofk.ch>

Lycée pilote Bourguiba de Tunis, Tunisia

Grade: 17.37/20 (5.2/6). Equivalent to the Swiss Matura.

Publications

Research publications and preprints

Skills & Tools

Technologies I use across research, development, and creative work.

Python PyTorch Deep Learning LLMs Molecular Docking React Next.js TypeScript Node.js PostgreSQL FastAPI Docker Linux / HPC Git scikit-learn AI Agents

Tools & Technologies

Programming Languages

  • Bash — Shell scripting & automation
  • C / C++ — Systems & scientific computing
  • CSS — Web design & layout
  • Go — Compiled language for efficiency
  • HTML — Web content structure
  • JavaScript / TypeScript — Web applications
  • Python — Data science, ML, web & automation
  • Rust — Safety-focused systems programming
  • SQL — Database querying

AI & Machine Learning

  • PyTorch — Deep learning framework
  • PyTorch Lightning — Scalable ML training
  • scikit-learn — Classical ML
  • Hugging Face — Models & datasets
  • Weights & Biases — Experiment tracking
  • Google Colab — Cloud notebooks
  • Jupyter — Interactive computing
  • OpenAI API — Language model APIs

Data Science & Visualization

  • NumPy — Numerical computing
  • Pandas — Data manipulation
  • SciPy — Scientific computing
  • Matplotlib — Plotting
  • Seaborn — Statistical visualization
  • Plotly — Interactive charts

Frontend

  • React — Component-based UI
  • Next.js — React SSR & SSG
  • Vue.js — Progressive framework
  • Nuxt — Vue SSR & SSG
  • TailwindCSS — Utility-first CSS
  • Bootstrap — Responsive framework
  • Material UI — React components

Backend

  • Node.js — JavaScript runtime
  • Express.js — Node web framework
  • FastAPI — Modern Python APIs
  • Django — Full-stack Python
  • Flask — Lightweight Python web

Databases

  • PostgreSQL — Relational database
  • SQLite — Lightweight file-based DB
  • MongoDB — Document database
  • Redis — In-memory cache & store
  • Neo4j — Graph database
  • Supabase — Open-source BaaS
  • Firebase — Realtime DB & Firestore

Cloud & DevOps

  • Vercel — Frontend deployment
  • Netlify — Web app hosting
  • Docker — Containerization
  • GitHub Actions — CI/CD workflows
  • Nginx — Web server & reverse proxy

Mobile & Desktop

  • React Native — Cross-platform mobile
  • Electron — Desktop apps with web tech
  • Qt — Cross-platform applications

Editor & Terminal

  • Cursor — AI-powered editor
  • VS Code — Extensible code editor
  • Neovim / Vim — Terminal editors
  • Warp — Modern terminal
  • Zsh — Shell
  • Tmux — Terminal multiplexer

AI Assistants

  • Anthropic Claude — AI assistant
  • ChatGPT — Conversational AI
  • GitHub Copilot — AI pair programming
  • Cursor AI — AI coding assistant

Dev Tools

  • Git — Version control
  • GitHub / GitLab — Code collaboration
  • Postman — API development
  • Prettier / Black — Code formatting
  • Pylint — Python linting
  • CMake — Build system
  • SQLAlchemy — Python ORM

Design & Prototyping

  • Figma — UI/UX design & prototyping
  • Canva — Graphic design

Productivity

  • Notion — Notes & docs
  • Obsidian — Knowledge base
  • Linear — Project tracking
  • Todoist — Task management
  • Google Calendar — Scheduling
  • Miro — Collaborative whiteboard

Creative

  • Logic Pro — Music production
  • GarageBand — Audio workstation
  • OBS Studio — Video recording & streaming
  • iMovie — Video editing

Hardware

  • MacBook Pro — Primary laptop
  • MacBook Air — Portable laptop
  • External Monitor — Extended display
  • Headphones — Audio

Methodologies

  • Test-driven development
  • Behavior-driven development
  • Spec-driven development
  • Scrum & Kanban
  • Microservices
  • REST API design