{"id":28328215,"url":"https://github.com/niaid/ace-2021","last_synced_at":"2026-01-26T13:02:47.107Z","repository":{"id":53591156,"uuid":"320627959","full_name":"niaid/ACE-2021","owner":"niaid","description":"African Centers of Excellence (ACE) Training for 2021","archived":false,"fork":false,"pushed_at":"2021-05-14T15:23:43.000Z","size":46,"stargazers_count":1,"open_issues_count":2,"forks_count":6,"subscribers_count":6,"default_branch":"main","last_synced_at":"2025-06-24T08:44:43.062Z","etag":null,"topics":["ace","bcbb-training","bioinformatics","metagenomics","sequencing"],"latest_commit_sha":null,"homepage":"https://niaid.github.io/ACE-2021/","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/niaid.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-12-11T16:34:21.000Z","updated_at":"2022-09-09T19:09:30.000Z","dependencies_parsed_at":"2022-08-31T19:11:03.321Z","dependency_job_id":null,"html_url":"https://github.com/niaid/ACE-2021","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/niaid/ACE-2021","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/niaid%2FACE-2021","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/niaid%2FACE-2021/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/niaid%2FACE-2021/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/niaid%2FACE-2021/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/niaid","download_url":"https://codeload.github.com/niaid/ACE-2021/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/niaid%2FACE-2021/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28778728,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-26T11:46:04.308Z","status":"ssl_error","status_checked_at":"2026-01-26T11:46:02.664Z","response_time":59,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["ace","bcbb-training","bioinformatics","metagenomics","sequencing"],"created_at":"2025-05-26T06:16:17.065Z","updated_at":"2026-01-26T13:02:47.091Z","avatar_url":"https://github.com/niaid.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# SCHEDULE\n\n| Instructor     | Subject                                     | Topic (Click to access materials, video)                                                                                                                                                                                                                                                                 | Originally Taught |\n| -------------- | ------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------- |\n| 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       |\n| 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       |\n| Y. Zhu         | High Throughput Sequencing and Analysis     | RNA-seq Part II, single-cell RNA-seq \u0026 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| 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       |\n| T. Armstrong   | Unix \u0026 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       |\n| T. Armstrong   | Unix \u0026 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       |\n| T. Armstrong   | Unix \u0026 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       |\n| A. Roy         | Unix \u0026 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       |\n| A. Roy         | Unix \u0026 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       |\n| A. Roy         | Unix \u0026 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       |\n| A. Roy         | Unix \u0026 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       |\n| A. Roy         | Unix \u0026 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       |\n\n# INSTRUCTORS\nComputational Biology Specialists from the National Institute of Allergy and Infectious Diseases (NIAID) will be teaching courses on bioinformatics topics and biocomputing tools.\n\n- Angelina Angelova, Ph.D.\\*\n- Tony Armstrong, Ph.D.\\*\n- Phil Cruz, Ph.D.\\*\n- Jingwen Gu, M.S.\\*\n- Brendan Jeffrey, Ph.D.\\*\n- Eric Karlins, Ph.D.\\*\n- Andrew Oler, Ph.D.\n- Mariam Quiñones, Ph.D.\n- Amit Roy, Ph.D.\\*\n- Poorani Subramanian, Ph.D.\\*\n- Dan Veltri, Ph.D.\n- Kurt Wollenberg, Ph.D.\\*\n- Yunhua Zhu, Ph.D.\\*\n\n\t\\* Instructors provide bioinformatics support at the NIAID as employees of Medical Science and Computing, Inc.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fniaid%2Face-2021","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fniaid%2Face-2021","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fniaid%2Face-2021/lists"}