Open to collaboration and opportunities

Computational methods for biology, and the infrastructure that runs them.

Postdoctoral researcher at Forschungszentrum Jülich, building small language models and agentic systems for mass spectrometry, including spectral annotation for lipidomics. Earlier work spans molecular dynamics and structure-based drug discovery, sequence indexing at petabyte scale, and three years running Galaxy Europe for over 170,000 researchers.

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Portrait of Sanjay Kumar Srikakulam

22

Publications, deliverables and reports

1,648

Zenodo downloads

11 yrs

Research and infrastructure

Work

Selected projects

Software and infrastructure I have built or contributed to.

AlphaFold2 non-Docker

AlphaFold2 ships as a Docker image, which requires root and is therefore unavailable on most shared HPC clusters. This is a setup that removes the Docker dependency.

  • Python
  • Shell
  • HPC
  • structure prediction

378Stars

125Forks

synced from source

MetaProFi

A chunked Bloom filter for protein and nucleotide sequence search. It accepts a bounded false-positive rate in exchange for an index small enough to hold in memory at petabyte scale.

  • Python
  • Bloom filters
  • sequence search

13Stars

2Forks

11Citations

synced from source

Galaxy Europe

Meta-scheduling, cloud infrastructure, deployment, and operations for the European Galaxy instance, which serves over 170,000 registered users.

  • Terraform
  • Ansible
  • OpenStack
  • HTCondor

25Stars

115Forks

synced from source

Open source

Most of my code lives in organisation repositories. A selection of the public ones I contribute to:

Experience

Education and roles

2024

PhD, Bioinformatics

Helmholtz Institute for Pharmaceutical Research Saarland and Saarland University, Saarbrücken, Germany

2018

M.Sc., Bioinformatics

Saarland University, Saarbrücken, Germany

2014

B.Tech., Bioinformatics

SRM University, Kancheepuram, India

201320162019202220252026
Project Assistant (Student)National Institute for Research in Tuberculosis, ICMR2013 to 2014
System Administrator (Research Assistant)German Research Centre for Artificial Intelligence (DFKI)2015 to 2022
System Administrator and DevOps, Bioinformatics IT Core FacilityHelmholtz Institute for Pharmaceutical Research Saarland2018 to 2023
BioinformaticianSaarland University Hospital2021 to 2022
Scientific Researcher (Postdoc)University of Freiburg2022 to 2025
Postdoctoral ResearcherForschungszentrum Jülich GmbH2025 to Present

09/2025 to Present

Postdoctoral Researcher

Forschungszentrum Jülich GmbH, Jülich, Germany

  • AI and agentic frameworks for biocuration of metabolomics and lipidomics literature: named entity recognition, ontologies, controlled vocabularies, and knowledge graphs.
  • SeqSidecar, a columnar query engine for nucleotide and protein sequencing reads, supporting filtering, search, deduplication, and remote index-based querying of FASTA and FASTQ at scale.
  • An OCI container registry with CVE scanning, SBOM generation, and image signing, run as a European service through de.NBI and ELIXIR.

de.NBIELIXIR GermanyEOSC UnitedEOSC EntrustNFDI

7 more responsibilities
  • Novel algorithms and data structures for indexing and querying petabyte-scale sequencing datasets.
  • Administration, strategic planning, and implementation of de.NBI infrastructure and services, focused on cloud infrastructure, AI, and agentic frameworks.
  • Administration and strategic expansion of de.NBI and ELIXIR Germany infrastructure and services.
  • Demonstrated EOSC EU Node use cases through the EOSC United project.
  • Part of the EOSC Entrust project, establishing blueprints for secure data processing environments.
  • Talks, posters, and workshops at national and international conferences.
  • Represented de.NBI and ELIXIR Germany in national initiatives (NFDI) and European Commission projects.

08/2022 to 08/2025

Scientific Researcher (Postdoc)

University of Freiburg, Freiburg, Germany

  • Administration and management of Galaxy Europe, supporting over 170,000 users.
  • Algorithms and optimisations for meta-scheduling, including reducing carbon footprint through efficient scheduling and distributed remote computing.
  • Configuration, deployment, administration, and maintenance of the Galaxy HPC OpenStack cloud using Terraform, Ansible, Jenkins, Rsyslog, and the TIG stack.
10 more responsibilities
  • Application development, feature innovation, and research.
  • Deliverables and reports for national and EU-funded initiatives.
  • Research data management through Galaxy.
  • Development and deployment of configurations through GitOps and Jenkins CI/CD.
  • Scripting and automation.
  • Infrastructure monitoring and performance analysis.
  • Troubleshooting, logging, and log analysis.
  • Support and documentation.
  • Partnering with collaborators on national and international projects.
  • Represented the organisation at conferences through exhibition booths, presentations, and scientific and industry discussions.

02/2021 to 02/2022

Bioinformatician

Saarland University Hospital, Homburg, Germany

  • Machine learning and survival analysis on longitudinal COPD patient data to identify biomarkers.
  • OMICS data analysis.

10/2018 to 03/2023

System Administrator and DevOps, Bioinformatics IT Core Facility

Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany

  • Setup, design, and establishment of the Bioinformatics IT core facility.
  • Installation, configuration, and maintenance of CentOS and Red Hat Linux HPC clusters, servers, desktops, and workstations.
  • Containerised web services (Gitea, MediaWiki, WordPress, Docker registry) and infrastructure monitoring through Icinga.
10 more responsibilities
  • Site reliability engineering processes.
  • Budgeting, purchasing, and inventory.
  • Bioinformatics application installation, configuration, deployment, and maintenance.
  • Support and documentation for all researchers.
  • On-demand compute provisioning, physical and virtual, with network and storage allocation.
  • Storage provisioning and administration.
  • MariaDB database server administration.
  • Ansible and custom RPM packages for configuration, monitoring, and maintenance.
  • Configuration of iDRAC/IPMI, DNS, TCP/IP, TLS/SSL, LDAP, Active Directory, SSH, Fail2ban, firewall, AutoFS, and printers.
  • Troubleshooting and resolution of hardware and software issues.

09/2015 to 03/2022

System Administrator (Research Assistant)

German Research Centre for Artificial Intelligence (DFKI), Saarbrücken, Germany

  • Development and maintenance of an RPM-based distributed configuration management system.
  • Development, configuration, and maintenance of web services including MediaWiki, WordPress, Gitea, and reverse proxies.
  • Configuration and maintenance of Jenkins build automation and KVM virtual machines.
7 more responsibilities
  • Development and maintenance of installation and configuration routines.
  • Configuration and maintenance of network monitoring through Icinga 2.
  • Development and maintenance of containerised applications using Docker.
  • Scripting and automation.
  • Monitoring and maintenance of workstations and servers.
  • Atlassian stack administration: Crowd, Jira, Confluence, and Bitbucket.
  • Support and documentation for the DFKI-ASR user community and the team.

05/2013 to 07/2014

Project Assistant (Student)

National Institute for Research in Tuberculosis, ICMR, Chennai, India

  • Maintained the Mycobacterium tuberculosis structural database (MtbSD).
  • Sequence and structural ensemble analysis of HIV and M. tuberculosis proteins.
  • Molecular modelling, drug design, and docking.
1 more responsibilities
  • Statistical analysis.

Technical skills

AI and LLM stack

vLLM, PydanticAI, coding agents, pgvector, OpenAI API

Certificate management

Let's Encrypt

CI/CD

Jenkins

Cloud DNS

AWS Route 53, DigitalOcean

Cloud platforms and services

OpenStack, AWS

Containers and virtualisation

Docker, LXC, KVM

Databases

SQL, MySQL/MariaDB, PostgreSQL

High-throughput workload scheduling

HTCondor

Infrastructure as code and configuration management

Terraform, Ansible, RPM packaging, Pulp

Monitoring and observability

Icinga, Telegraf, InfluxDB, Grafana

Programming

Python, Shell scripting (Bash), R

Security

Firewall management, SSL/TLS certificates, Fail2ban

Storage

NAS, DAS, JBOD, NFS, S3, CVMFS

Version control

Git

Web servers

Apache, Nginx

Research

Publications and outputs

Journal articles, conference papers, preprints, and project deliverables.