https://github.com/niaid/ace-2021
African Centers of Excellence (ACE) Training for 2021
https://github.com/niaid/ace-2021
ace bcbb-training bioinformatics metagenomics sequencing
Last synced: 5 months ago
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African Centers of Excellence (ACE) Training for 2021
- Host: GitHub
- URL: https://github.com/niaid/ace-2021
- Owner: niaid
- License: mit
- Created: 2020-12-11T16:34:21.000Z (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2021-05-14T15:23:43.000Z (over 4 years ago)
- Last Synced: 2025-06-02T15:17:19.215Z (6 months ago)
- Topics: ace, bcbb-training, bioinformatics, metagenomics, sequencing
- Homepage: https://niaid.github.io/ACE-2021/
- Size: 44.9 KB
- Stars: 1
- Watchers: 6
- Forks: 6
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# SCHEDULE
| Instructor | Subject | Topic (Click to access materials, video) | Originally Taught |
| -------------- | ------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------- |
| E. Karlins | High Throughput Sequencing and Analysis | Public projects based on human NGS data (Human genome, HapMap, population genetics, variations…) [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7105-Sequencing/24-Feb-2021_Public_NGS_Projects.pdf) [ Video)](https://youtu.be/ja7HrcqFf5E) | 24-Feb-2021 |
| B. Jeffrey | High Throughput Sequencing and Analysis | Processing of aligned reads for RNA-seq [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7105-Sequencing/03-Mar-2021_RNAseq-main.zip) [ Video)](https://youtu.be/HSyiNSA1u-0) | 03-Mar-2021 |
| Y. Zhu | High Throughput Sequencing and Analysis | RNA-seq Part II, single-cell RNA-seq & pathway analysis [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7105-Sequencing/05-Mar-2021_singleCellRNA-seq.pdf) [ Video)](https://youtu.be/EZwgYT_r0QY) | 05-Mar-2021 |
| A. Angelova | High Throughput Sequencing and Analysis | Metagenomics overview (Metataxonomics) [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7105-Sequencing/10-Mar-2021_WGS-Metagenomics_16S.pdf) [ Video)](https://youtu.be/UrIyWtOwLwg) | 10-Mar-2021 |
| P. Subramanian | High Throughput Sequencing and Analysis | Cyber environments for the processing and analysis of NGS data [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7105-Sequencing/) [ Video)](waiting) | 17-Mar-2021 |
| P. Subramanian | High Throughput Sequencing and Analysis | Managing data and simple analyses in the Galaxy cyber-environment (Practical) [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7105-Sequencing/GalaxyACEMakerereTraining_22Mar2021.html) [ Video)](https://youtu.be/SE0yjXMvQXk) | 22-Mar-2021 |
| A. Angelova | High Throughput Sequencing and Analysis | Metagenomics overview (Shotgun metagenomics) [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7105-Sequencing/08-April-2021_MSB7105_Metagenomics.pdf) [ Video)](https://youtu.be/DsVnaD8QeSo) | 08-Apr-2021 |
| A. Angelova | High Throughput Sequencing and Analysis | Functional metagenomics - WGS [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7105-Sequencing/metagenomics_practical.zip) [ Video)](https://youtu.be/Y_xkjHniyGs) | 12-Apr-2021 |
| H. Lorenzi | Molecular Biology for Bioinformatics | Nucleic Acid Techniques and Tools 1: Intro to NGS and Sanger sequencing [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7101-MolBiol/Introduction_to_NGS_ACE_small_02-Mar-2021.pdf) [ Video)](https://youtu.be/tqGIeQlzcGc) | 26-Feb-2021 |
| H. Lorenzi | Molecular Biology for Bioinformatics | Nucleic Acid Techniques and Tools 1: Intro to NGS and Sanger sequencing [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7101-MolBiol/Introduction_to_NGS_ACE_small_02-Mar-2021.pdf) [ Video)](https://youtu.be/7DkUxAYHrpU) | 02-Mar-2021 |
| K. Wollenberg | Molecular Biology for Bioinformatics | Genetic evolution/diversity mechanisms - Part I [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7101-MolBiol/GeneticEvolutionDiversityMechanisms.pdf) [ Video)](https://youtu.be/AgPFaJiikiw) | 14-Apr-2021 |
| K. Wollenberg | Molecular Biology for Bioinformatics | Genetic evolution/diversity mechanisms - Part II [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7101-MolBiol/GeneticEvolutionDiversityMechanisms.pdf) [ Video)](https://youtu.be/g3nSz1iTBnY) | 19-Apr-2021 |
| M. Quinones | Molecular Biology for Bioinformatics | Nucleic Acid Techniques and Tools 2: Practical on Sanger or QC of NGS [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7101-MolBiol/MolecularBiology_22-April-2021.zip) [ Video)](https://youtu.be/qHS1_re8M5Y) | 22-Apr-2021 |
| A. Oler | Online bioinformatics and sequence database | Genome browsers [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7104-SequenceDatabase/Genome-Browsers-main_23Feb2021.zip) [ Video)](https://youtu.be/ojsOS4t0Epk) | 23-Feb-2021 |
| M. Quinones | Online bioinformatics and sequence database | Primary sequence databases - Part I [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7104-SequenceDatabase/Sequence_databases_partI_and_partII_04-08-Mar-2021.pdf) [ Video)](https://youtu.be/L2QCurau8sw) | 04-Mar-2021 |
| M. Quinones | Online bioinformatics and sequence database | Primary sequence databases - Part II [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7104-SequenceDatabase/Sequence_databases_partI_and_partII_04-08-Mar-2021.pdf) [ Video)](https://youtu.be/wZ83jaHNa4E) | 08-Mar-2021 |
| A. Roy | Online bioinformatics and sequence database | Protein databases [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7103-Unix/Uniprot_06_April_2021.pptx) [ Video)](https://youtu.be/Ur4k7nItmK8) | 06-Apr-2021 |
| A. Roy | Online bioinformatics and sequence database | Protein databases [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7103-Unix/Uniprot_06_April_2021.pptx) [ Video)](https://youtu.be/YG3Wg0JaFaY) | 07-Apr-2021 |
| M. Quinones | Online bioinformatics and sequence database | Advanced literature search (PubMed) [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7104-SequenceDatabase/PubMed_search_15-April-2021.pdf) [ Video)](https://youtu.be/Y8XPMVM1Ykc) | 15-Apr-2021 |
| M. Quinones | Online bioinformatics and sequence database | Sequence retrieval tools (SRA) [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7104-SequenceDatabase/Sequence_retrieval_21-April-2021.pdf) [ Video)](https://youtu.be/oanj7AeZBJA) | 21-Apr-2021 |
| P. Cruz | Online bioinformatics and sequence database | Cheminformatics (Chemical compound – drug discovery) Lecture [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7104-SequenceDatabase/Cheminformatics.zip) [ Video)](https://youtu.be/Rqs4uOGGUI0) | 27-Apr-2021 |
| P. Cruz | Online bioinformatics and sequence database | Cheminformatics (Chemical compound – drug discovery) Demo [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7104-SequenceDatabase/Cheminformatics.zip) [ Video)](https://youtu.be/YsK9hI7Lj_0) | 28-Apr-2021 |
| J. Gu | R programming and Bioconductor | Generating data and manipulating objects - Part I [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7102-RProgramming/09-Mar-2021_part1_Introduction_to_R.zip) [ Video)](https://youtu.be/CG73IzLS9b4) | 09-Mar-2021 |
| P. Subramanian | R programming and Bioconductor | Generating graphics in R - Part I [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7102-RProgramming/12-Mar-2021_r_graphics_part1plus.zip) [ Video)](https://youtu.be/ex41xNHxD3w) | 12-Mar-2021 |
| J. Gu | R programming and Bioconductor | Generating data and manipulating objects - Part II [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7102-RProgramming/09-Mar-2021_part1_Introduction_to_R.zip) [ Video)](https://youtu.be/Rf_W8r6c9VM) | 16-Mar-2021 |
| D. Veltri | R programming and Bioconductor | Introduction to R markdown - Part I [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7102-RProgramming/intro-to-rmarkdown.zip) [ Video)](https://youtu.be/WtRymLiP6Lw) | 24-Mar-2021 |
| P. Subramanian | R programming and Bioconductor | Generating graphics in R - Part II [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7102-RProgramming/12-Mar-2021_r_graphics_part1plus.zip) [ Video)](https://youtu.be/edyCfE96yP8) | 26-Mar-2021 |
| J. Gu | R programming and Bioconductor | Introduction to Statistical Analysis in R - Part I [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7102-RProgramming/stat_programming.zip) [ Video)](https://youtu.be/4ifqp3T1r1M) | 31-Mar-2021 |
| J. Gu | R programming and Bioconductor | Introduction to Statistical Analysis in R - Part II [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7102-RProgramming/stat_programming.zip) [ Video)](https://youtu.be/1_wcKq-U8wU) | 05-Apr-2021 |
| D. Veltri | R programming and Bioconductor | Introduction to R markdown - Part II [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7102-RProgramming/intro-to-rmarkdown.zip) [ Video)](https://youtu.be/mehiEnvV_DA) | 13-Apr-2021 |
| T. Armstrong | Unix & Shell Scripting | Introduction to UNIX and Text Editing [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7103-Unix/Intro_to_Unix_25_Feb_2021.pdf) [ Video)](https://youtu.be/DWE_fC7OVMM) | 25-Feb-2021 |
| T. Armstrong | Unix & Shell Scripting | Introduction to UNIX editors: Vi [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7103-Unix/Intro_to_Vi_March_2021.zip) [ Video)](https://youtu.be/Ob-USkwBGzg) | 01-Mar-2021 |
| T. Armstrong | Unix & Shell Scripting | Introduction to UNIX editors: Vi Advanced Topics [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7103-Unix/Intro_to_Vi_March_2021.zip) [ Video)](https://youtu.be/5Rkmb1S372U) | 11-Mar-2021 |
| A. Roy | Unix & Shell Scripting | Manipulating files and data on Linux [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7103-Unix/bash_scripting_15_March_2021.zip) [ Video)](https://youtu.be/ncZWthSkr2I) | 15-Mar-2021 |
| A. Roy | Unix & Shell Scripting | Shell Scripting/Programming - Part I [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7103-Unix/bash_scripting_19_March_2021.zip) [ Video)](https://youtu.be/OGmB37OakpY) | 19-Mar-2021 |
| A. Roy | Unix & Shell Scripting | Shell Scripting/Programming - Part II [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7103-Unix/bash_scripting_19_March_2021.zip) [ Video)](https://youtu.be/le_hsg-i1z0) | 23-Mar-2021 |
| A. Roy | Unix & Shell Scripting | Introduction to Awk and Sed programming - Part I [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7103-Unix/sed_awk_29_March_2021.zip) [ Video)](https://youtu.be/meuxCpANEZw) | 29-Mar-2021 |
| A. Roy | Unix & Shell Scripting | Introduction to Awk and Sed programming - Part II [(Materials,](https://niaid.github.io/nbp_training_resources/ace/MSB7103-Unix/sed_awk_29_March_2021.zip) [ Video)](https://youtu.be/t49TP4Ie1zU) | 30-Mar-2021 |
# INSTRUCTORS
Computational Biology Specialists from the National Institute of Allergy and Infectious Diseases (NIAID) will be teaching courses on bioinformatics topics and biocomputing tools.
- Angelina Angelova, Ph.D.\*
- Tony Armstrong, Ph.D.\*
- Phil Cruz, Ph.D.\*
- Jingwen Gu, M.S.\*
- Brendan Jeffrey, Ph.D.\*
- Eric Karlins, Ph.D.\*
- Andrew Oler, Ph.D.
- Mariam Quiñones, Ph.D.
- Amit Roy, Ph.D.\*
- Poorani Subramanian, Ph.D.\*
- Dan Veltri, Ph.D.
- Kurt Wollenberg, Ph.D.\*
- Yunhua Zhu, Ph.D.\*
\* Instructors provide bioinformatics support at the NIAID as employees of Medical Science and Computing, Inc.