我们的基因体时代-AI, Data和生物资讯 Overview

大家好，我们的基因体时代是我之前一直在经营的部落格名称，假如对於生物资讯、合成生物学、基因体学、资料视觉化、R有兴趣的话，可以来参观参观，也欢迎同好多多交流，这次来报名2021年的铁人赛，想挑战一下来撰写生物资讯中关於AI和Data的角度，应该会颇有趣且深具挑战，let's writing to learn！

起手式，先来架构一下，这个月的计画，然後相关的阅读参考

第一周：2021/9/01 - 2021/9/05（5天）

• Knowledge-这一周先以大范围的介绍机器学习在基因体学中的角色、大数据在生医领域、合成生物学中的生物资讯

第二周：2021/9/06 - 2021/9/12（7天）

• Data-分子生物学、基因体学中的资料格式

第三周：2021/9/13 - 2021/9/19（7天）

• Tools-介绍Bioconductor和其ecosystem的工具和资料结构

第四周：2021/9/21 - 2021/9/26（7天）

• Advance topis in AI using in life science

第五周：2021/9/27 - 2021/9/30（4天）

• let's tackle COVID-19 with AI and Data

重要的点

• Tools used in Molecular Biology: Benchling, Snapgene
• Synthetic biology design tools
• Bioconductor
• Tidyverse
• NIH API, Unix tools
• Biopython
• GATK
• Common workflow Langugage
• Cloud tools
• 台湾超级电脑

学习参考：
Resources

• AnVIL: NIGRI Analysis Visualization and Informatics Lab-space
• MIT Computational Systems Biology: Deep Learning in the Life Science
• Applied Computational Genomics Course at UU: Spring 2021
• PH525x series-Biomedical Data Science
  Books
• The Biostar Handbook 2nd, 2021
• Modern Statistics for Modern Biology, 2021
• Genomics in the Cloud, 2020
• Computing Skills for Biologist: A toolbox, 2019
• Computer Age Statistical Inference: Algorithms, Evidence, and Data Science, 2016
• The Biostar Handbook: Bioinformatics Data Analysis Guide, 2016
• Bioinformatics Data Skills, 2015
• Muhammad A. Alam (2019), "ECE 695E: An Introduction to Data Analysis, Design of Experiment, and Machine Learning," https://nanohub.org/resources/28817.

Talks

• National Human Genome Research Institute: Machine Learning in Genomics: Tools, Resources, Clinical Applications and Ethics

  • What are the opportunities and challenges for ML in genomics research?
  • Algorithm development and machine learning approaches in genomics
  • Ethical, Legal and Social Implications of machine learning in genomics
  • Data and resource needs for machine learning in genomics
  • Machine learning i clinical genomics

• Bioinformatics DotCa：Machine Learning workshop May 25 - 26 2021, Youtube list

• MIT Computational Systems Biology: Deep Learning in the Life Science
  *nanoHUB
  Course

• Hacking COVID-19 - Course 1: Identifying a Deadly Pathogen

• Hacking COVID-19 - COurse 2: Decoding SARS-CoV-2's Secrets

• Access Bioinformatics Databases with Biopython

• 3D SARS-CoV-19 Protein Visualization With Biopython

• SARS-CoV-2 Protein Modeling and Drug Docking