adam
mleap
| adam | mleap | |
|---|---|---|
| 3 | 1 | |
| 967 | 1,494 | |
| 0.2% | 0.1% | |
| 6.1 | 5.2 | |
| about 1 month ago | 6 months ago | |
| Scala | Scala | |
| Apache License 2.0 | Apache License 2.0 |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
adam
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biobear -- python package with minimal dependencies for bioinformatic file parsing and querying using rust and polars as the backend
FYI: ADAM seems to do that
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Advanced Scientific Data Format
We presented using Parquet formats for bioinformatics 2012/13-ish at the Bioinformatics Open Source Conference (BOSC) and got laughed out of the place.
While using Apache Spark for bioinformatics [0] never really took off, I still think Parquet formats for bioinformatics [1] is a good idea, especially with DuckDB, Apache Arrow, etc. supporting Parquet out of the box.
0 - https://github.com/bigdatagenomics/adam
1 - https://github.com/bigdatagenomics/bdg-formats
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Seq: A programming language for high-performance computational genomics
We're here, still plugging along.
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
https://github.com/bigdatagenomics/adam
mleap
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Machine Learning Pipelines with Spark: Introductory Guide (Part 1)
Everything is custom and will take a lot of work, but luckily, you don’t have to do all the work here. In THE second article, you will use MLeap, a library that does the heavy lifting in terms of serializing Spark ML Pipeline for real-time inference and also provides an execution engine for Spark so you can deploy pipelines on non-Spark runtimes.
What are some alternatives?
seq - A high-performance, Pythonic language for bioinformatics
Apache Spark - Apache Spark - A unified analytics engine for large-scale data processing
bioconda-recipes - Conda recipes for the bioconda channel.
Pandas - Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
nimconf2021 - Slides for Nimconf21
spark-nlp - State of the Art Natural Language Processing
asdf - ASDF (Advanced Scientific Data Format) is a next generation interchange format for scientific data
kubernetes - Production-Grade Container Scheduling and Management
cramino - A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
scikit-learn - scikit-learn: machine learning in Python
uvfs - Microscopic C++20 archive format
BigDL - Accelerate local LLM inference and finetuning (LLaMA, Mistral, ChatGLM, Qwen, Baichuan, Mixtral, Gemma, etc.) on Intel CPU and GPU (e.g., local PC with iGPU, discrete GPU such as Arc, Flex and Max). A PyTorch LLM library that seamlessly integrates with llama.cpp, Ollama, HuggingFace, LangChain, LlamaIndex, DeepSpeed, vLLM, FastChat, etc.