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codecreatede/README.md

About me

  • Accepting position on Scientist/Academics/Researcher/Specialist/System Administration.
  • Curriculum Vitae/Past Employers References, Scopus, ORCID, Web of Science.
  • Extremely collaborative and I only supports those who support me and take right approaches. Highly Communicative, approachable, motivated, task and solution oriented, time responsive, and initiative taker.
  • I dont use AI for code writing and I am a very frequent writer at Linux community.
  • You can read this to understand how to avoid fake and how to invest in real people Getting to know ahead.
  • If you havent heard or confirmed with me and believed anything, you have heard from wrong/false/fake people.Deciding my personal preferences/choices/likes/dislikes is not anyone role and neither i will consider nor i will give importance. No one has the right to make a decision for me based on their thinking/assumptions. Dont waste others time and dont waste my time. You are wasting your time by listening to such people and that has nothing to do with me as i dont give importance to those people.

Scientific/Academic Research:Plant, Bacterial, Fungal Bioinformatics, Deep Learning,and DevOPs.

  • 2024 onwards: Universitat Potsdam, Germany, where I am currently based and self-learnt Julia, GO and Javascript. I benchmarked PacBioHifi genome analysis with complete web-based real time monitoring invoking javascript/HTML-CSS, and coded several packages, gems in Python, Ruby, Julia, GO. Self-learning Geospatial Application Development in Python and Javascript.
  • 2022-2023: I added several new skills as a carrier advancement and added machine and deep learning, added certification on devops and self-learnt Python, Web and Application development.
  • 2020-2021: Finnish Museum of Natural History and the University of Helsinki, Finland. I managed the sequencing used the NextSeq methods, including sequencing library methods. I completed genome assembly, annotations, markers genes, ITS, and phylogenomics of over 500 different species.
  • 2017-2021: Finnish Museum of Natural History and University of Helsinki, Finland conducting research on genome bioinformatics and sequencing the genomes of lower plants, including Coleochaete orbicularis, Blasia pusilla, Chaetospiridium orbicularis, Polytrichum commune, Mallomonas, and Cryptomonas species, in which I did pacbio sequencing, assembly, annotations, organelle genomes and evolutionary/phylogenomic/comparative genomics approaches. Additionally, during that tenure, I worked for collaborations with the host organization such as Edinburgh UK, to analyse the genomics data for PAFTOL species and the chloroplast genomes of the Ambrosia clade from Norway.
  • 2016-2017: University of Connecticut, USA, where i analyzed the Douglas fir genome from the genome annotation to the phylogenomics and identifying genes and evolution of importance.
  • 2014–2016: University of Technology, Sydney, Australia, where I developed computational methods for understanding seagrasses.
  • 2011-2014: Fondazione Edmund Mach, Italy, where I developed and analyzed bioinformatics methods for transcriptional and post-transcriptional genomics across nuclear and organelle genomes. I analyzed multiple metagenomics anlaysis coming from the fungal and bacterial species involving ITS metagenomics, as well as the bacterial genome metagenomics.

Scientific/Application/System Administration:

  • All code and ideas concieved and written by me unless specified.
  • Prior to 2021: all code internally hosted by work places.
  • Till 2021: C++, Bash, Awk, R.
  • From 2021-2024: Bash, Awk, Python, Ruby, Julia, Javascript, GO.
  • July 2024 onwards: R and Ruby read and Mainstream Code - Bash, Awk, Python, Julia, Javascript, GO
  • Bioinformatics,Deep Learning : Bash/Shell, Awk, Python, Julia, Javascript, GO
  • Machine/Deep Learning: PyTorch, Tensorflow, XGBoost, Scikit-learn, Keras, LightGBM, Fastai.
  • Package Development: Python, Julia, GO API Development: FASTAPI. Documentation: Markdown, MkDocs, HUGO, Quatro.
  • DevOPs/System Administration: Bash, Awk, Python, GO. Code Management: Git, GitKraken Orchestration:Terraform, Kubernetes. Visualization: Grafana. LDAP: LDAPManagement and Server configuration
  • Database: SQlite3, PostgresSQL, MongoDB. HPC and Containerization: PBS, SLURM, Apptainer, Docker
  • Web Application Develpoment: Shiny/ShinyExpress(Python), Streamlit, Django, Julia, Flask, Javascript.
  • Geospatial Application Developement: Python, Javascript
  • Application Development: Javascript, Python, GO
  • Operating System and Code Editor: Fedora, Neovim/NeoVide, Cursor.
  • Terminal: Wezterm, tMUX, Zellij.

Package/Application Development:

Pinned Loading

  1. genomeassembly-pacbiohifi genomeassembly-pacbiohifi Public

    PacbioHifi genome assembly benchmarks

    HTML

  2. go-pacbiohifi go-pacbiohifi Public

    profiling pacbiokmers and filtering pacbio kmers

    Go

  3. python-datastructure python-datastructure Public

    my approach of solving the leetcode, interviewcode and other questions

    Python

  4. sqlite3-genome sqlite3-genome Public

    python implementation of sqlite3 for genome assembly

    Python

  5. tairaccession tairaccession Public

    python package for arabidopsis genome analysis

    Python

  6. trie-suffixarray.jl trie-suffixarray.jl Public

    generating the suffix arrays for all the pacbiohifi reads

    Julia