{"id":21023873,"url":"https://github.com/biogenies/seminar","last_synced_at":"2025-03-13T18:20:24.069Z","repository":{"id":40643457,"uuid":"276325072","full_name":"BioGenies/seminar","owner":"BioGenies","description":null,"archived":false,"fork":false,"pushed_at":"2025-01-16T09:55:33.000Z","size":39962,"stargazers_count":8,"open_issues_count":0,"forks_count":5,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-08T17:55:33.513Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BioGenies.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-07-01T08:45:09.000Z","updated_at":"2025-01-16T09:55:35.000Z","dependencies_parsed_at":"2024-08-27T12:07:08.338Z","dependency_job_id":null,"html_url":"https://github.com/BioGenies/seminar","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Fseminar","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Fseminar/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Fseminar/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Fseminar/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BioGenies","download_url":"https://codeload.github.com/BioGenies/seminar/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243456641,"owners_count":20293906,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":[],"created_at":"2024-11-19T11:20:44.218Z","updated_at":"2025-03-13T18:20:24.061Z","avatar_url":"https://github.com/BioGenies.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"## Seminars\n1. 18-03-2025: **advancements in developing model**, Sonor Kubkowski.\n1. 11-03-2025: **swirl tutorial**, Joanna Pokora.\n2. 25-02-2025: **Michałs video presentation**, Michał Burdukiewicz.\n1. 14-01-2025: **Metabocrates**, Joanna Pokora and Krystyna Grzesiak.\n1. 07-01-2025: **BioGenies plans for 2025**, Michał Burdukiewicz.\n1. 17-12-2024: **BioGenies year 2024 summary**, Jarek Chilimoniuk.\n1. 26-11-2024: **Our self-presentations part 2**, BioGenies.\n1. 19-11-2024: **Our self-presentations**, BioGenies.\n1. 12-11-2024: **OneTick**, Michał Burdukiewicz.\n1. 04-11-2024: just talking and having fun.\n1. 30-09-2024:\n1. 23-09-2024: no seminar.\n1. 16-09-2024: no seminar.\n1. 09-09-2024: just talking and having fun.\n1. 02-09-2024: **AmyloGraph 2.0 - data collection ideas**, Michał Burdukiewicz.\n1. 26-08-2024: **AmyloGraph 2.0 - project ideas**, Michał Burdukiewicz.\n1. 19-08-2024: **Funny stories**, Weronika Puchała, Jakub Kołodziejczyk.\n1. 12-07-2024: **BioGenies website ideas**, Jarek Chilimoniuk.\n1. 05-07-2024: no seminar.\n1. 01-07-2024: **Metabocrates**, Filip Gaj | **Pathway analysis tailored for metabolomic data**, Joanna Pokora.\n1. 24-06-2024: no seminar.\n1. 17-06-2024: **Miniatura grant**, Michał Burdukiewicz.\n1. 16-06-2024: Long lack of planned seminars because Michał was traveling and other things.\n1. 08-01-2024: **BioGenies in 2024**, Michał Burdukiewicz.\n1. 18-12-2023: **THE SEMINAR**, Oriol Bárcenas.\n1. 20-11-2023: **Robust dataset generation and feature characterization for the specific prediction and benchmarking of client and driver proteins in LLPS**, Carlos Pintado-Grima.\n1. 13-11-2023: **Deep neural networks (Understanding Deep Learning, Chapter 8)**, Jakub Kała.\n1. 04-11-2023: no seminar.\n1. 30-10-2023: **BioGenies update #10**, Michal Burdukiewicz.\n1. 23-10-2023: **Cracking the black box of deep sequence-based protein-protein interaction prediction**, Judith Bernett.\n1. 16-10-2023: **Cracking the black box of deep sequence-based protein-protein interaction prediction (pre-print comments)**, Jarosław Chilimoniuk.\n1. 09-10-2023: **Analysis of amyloid-amyloid interaction networks**, Laura Bąkała.\n1. 02-10-2023: **Tree of science**, Michał Burdukiewicz.\n1. 25-09-2023: **Deep neural networks (Understanding Deep Learning, Chapter 7)**, Jakub Kała.\n1. 18-09-2023: **Symptome Checkers**, Michał Burdukiewicz.\n1. 11-09-2023: **Deep neural networks (Understanding Deep Learning, Chapter 6)**, Jakub Kała.\n1. 21-08-2023: **Copernican Revolution**, Michał Burdukiewicz.\n1. 18-08-2023: **BioGenies: Year 3**.\n1. 14-08-2023: no seminar, we move it to 18-08-2023.\n1. 07-08-2023: **Deep neural networks (Understanding Deep Learning, Chapter 6)**, Jakub Kała.\n1. 31-07-2023: **Deep neural networks (Understanding Deep Learning, Chapter 5): notebooks**, Jakub Kała.\n1. 17-07-2023: **BioGenies update #9**, Michal Burdukiewicz.\n1. 10-07-2023: **Deep neural networks (Understanding Deep Learning, Chapter 4): notebooks**, Michal Burdukiewicz.\n1. 03-07-2023: **Styles with Benefits. The StyloMetrix Vectors for Stylistic and Semantic Text Classification of Small-Scale Datasets and Different Sample Length**, Inez Okulska.\n1. 26-06-2023: **Shallow neural networks (Understanding Deep Learning, Chapter 3): notebooks**, Jakub Kała.\n1. 19-06-2023: ~~**Shallow neural networks (Understanding Deep Learning, Chapter 3): notebooks**, Jakub Kała.~~ (Michał was not available)\n1. 12-06-2023: **Shallow neural networks (Understanding Deep Learning, Chapter 3)**, Jakub Kała.\n1. 05-06-2023: **Supervised learning (Understanding Deep Learning, Chapter 2)**, Michał Burdukiewicz.\n1. 19-05-2023: **When quality does not matter: a curious case of the subplastid location prediction**, Michał Burdukiewicz\n1. 12-05-2023: **Grantopisanie**, Michał Burdukiewicz.\n1. 17-04-2023 (maybe): **Introduction to metabolomics**, Michał Ciborowski (in Polish).\n1. 03-04-2023: **Preludium to science**, Jarosław Chilimoniuk \u0026 Krystyna Grzesiak.\n1. 27-03-2023: **Prediction of adhesins**, Katarzyna Sidorczuk.\n1. 20-03-2023: **Imputomics**, Jarosław Chilimoniuk.\n1. 13-03-2023: **Introduction to metabolomics**, Michał Ciborowski (in Polish).\n1. 06-03-2023: \n1. 27-02-2023: \n1. 20-02-2023: **Mining the entire space of peptide sequences**, Michał Burdukiewicz and Jakub Kała.\n1. 13-02-2023: **A heuristic algorithm solving the mutual-exclusivity sorting problem**, Alessandro Vinceti.\n1. 06-02-2023: **Optimal ensemble selection, part 2**, Michał Burdukiewicz.\n1. 30-01-2023: no seminar, only update.\n1. 23-01-2023: **Optimal ensemble selection**, Michał Burdukiewicz.\n1. 16-01-2023: **Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?**, Carlos Alberto Brizuela Rodríguez.\n1. 10-01-2023: **BioGenies in 2023**.\n1. 12-12-2022: ~~**Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?**, Carlos Alberto Brizuela Rodríguez.~~ only update.\n1. 05-12-2022: **AMPLE: detection of antimicrobial peptides in metagenomic data** Michał Burdukiewicz.\n1. 28-11-2022: **Lessons from Poland** Michał Burdukiewicz.\n1. 21-11-2022: no seminar, Michał is still networking in Warsaw.\n1. 14-11-2022: no seminar, Michał is networking in Warsaw.\n1. 07-11-2022: no seminar, Michał is networking in Białystok.\n1. 31-10-2022: **Your scariest research** BioGenies.\n1. 26-10-2022: no seminar, Michał is networking in Wrocław.\n1. 17-10-2022: **Pitfalls of machine learning for peptide analysis**, Michał Burdukiewicz.\n1. 10-10-2022: **The dynamic landscape of peptide function prediction** Oriol Bárcenas, Michał Burdukiewicz, Carlos Pintado-Grima.\n1. 03-10-2022: **BioGenies update #8**, Michał Burdukiewicz.\n1. 26-09-2022: **DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides**, Heng Zheng (MS Teams).\n1. 19-09-2022: no seminar, Michał has fun at the ECCB2022.\n1. 12-09-2022: no seminar, Michał has fun at the Barcelona Aggregation Training School.\n1. 05-09-2022: **Optimal prediction of antimicrobial peptides, part 2**, Michał Burdukiewicz.\n1. 29-08-2022: **Optimal prediction of antimicrobial peptides**, Michał Burdukiewicz.\n1. 22-08-2022: **PlastoGram v2**, Katarzyna Sidorczuk.\n1. 15-08-2022: Public holidays.\n1. 08-08-2022: **PlastoGram v1**, Katarzyna Sidorczuk.\n1. 02-08-2022: **BioGenies update #7**, Michał Burdukiewicz.\n1. 25-07-2022: **Empirical Bayes functional models for hydrogen deuterium exchange mass spectrometry**, Oliver M Crook.\n1. 18-07-2022: **Transfer learning in proteins: evaluating novel protein learned representations for bioinformatics tasks**, Emilio Fenoy.\n1. 11-07-2022: **Do deep learning models make a difference in the identification of antimicrobial peptides?**, Carlos Alberto Brizuela Rodríguez.\n1. 04-07-2022: **Inside the web of science**, Michał Burdukiewicz.\n1. 27-06-2022: **golem**, Dominik Rafacz \u0026 Gustav Meyrink.\n1. 20-06-2022: **bookdown**, Krystyna Grzesiak.\n1. 13-06-2022: no seminar, only update. \n2. 06-06-2022: no seminar, only update.\n3. 30-05-2022: **Zastosowania zautomatyzowanej kuracji jakości danych w modelowaniu systemów immunoinformatycznych opartym na uczeniu maszynowym**, Dominik Rafacz.\n4. 23-05-2022: no seminar, only update.\n5. 16-05-2022: **Modularizing Shiny**, Dominik Rafacz.\n6. 09-05-2022: **Analiza wpływu czynników środowiskowych oraz zanieczyszczeńpowietrza na choroby układu otolaryngologicznego na podstawie kohorty wrocławskiej z 2015 roku**, Dominik Nowakowski\n7. 25-04-2022: **Shiny intro**, Michał Burdukiewicz.\n8. 11-04-2022: **Effective presentations**, Mariusz Trojanowski.\n9. 04-04-2022: no seminar, only update.\n10. 28-03-2022: **Peer-review principles**, Michał Burdukiewicz.\n11. 21-03-2022: no seminar, only update.\n12. 14-03-2022: no seminar, only update.\n13. 07-03-2022: **Michał talks about things**, Michał Burdukiewicz.\n14. 02-03-2022: no seminar, only update.\n15. 16-02-2022: no seminar, only update.\n16. 09-02-2022: no seminar, only update.\n17. 02-02-2022: **AmyloGraph: Michał nie umie w zarządzanie**, Michał Burdukiewicz. \n18. 26-01-2022: **protti: an R package for comprehensive data analysis of peptide- and protein-centric bottom-up proteomics data**, Jan-Philipp Quast. \n19. 19-01-2022: **New Year's Resolutions**, Michał Burdukiewicz.\n20. 22-12-2021: **Memomikołajki**, BioGenies.\n21. 15-12-2021: **BioGenies update #6**, Michał Burdukiewicz.\n22. 08-12-2021: **Molecular Insights into the Differential Dynamics of SARS-CoV-2 Variants of Concern (VOC)**, Nabanita Mandal.\n23. 01-12-2021: **Applications of automated data quality curation in machine learning based modelling of immunoinformatic systems: Episode One**, Dominik Rafacz.\n24. 24-11-2021: **adhesiomeR**, Katarzyna Sidorczuk.\n25. 17-11-2021: **Peptipedia**, David Medina-Ortiz (new time: 3 PM UTC+2).\n26. 10-11-2021: **Building HMM and molecular docking analysis for the sensitive detection of anti-viral pneumonia antimicrobial peptides (AMPs)**, \nOlalekan Bakare.\n1. 03-11-2021: **Blood-brain barrier peptides**, Michał Burdukiewicz.\n1. 27-10-2021: **LILOP 2.0: I am choosing my hair color**, Michał Burdukiewicz.\n1. 20-10-2021: **Poster session at IBB**, BioGenies.\n1. 13-10-2021: **My own github profile readme**, Michał Burdukiewicz.\n1. 06-10-2021: **Protein-peptide docking in the era of accurate structure-prediction**, Sebastian Kmiecik.\n1. 29-09-2021: **Why my research is bad?**, Michał Burdukiewicz. \n1. 22-09-2021: no seminar, only update.\n1. 15-09-2021: **AmyloGraph: a comprehensive database of amyloid-amyloid interactions**, Michał Burdukiewicz. \n1. 08-09-2021: **Novel project managment**, Krystyna Grzesiak, Weronika Puchała.\n1. 01-09-2021: **Wstęp do modeli liniowych**, Krystyna Grzesiak. \n1. 25-08-2021: **Next grants**, Michał Burdukiewicz. \n1. 18-08-2021: **Elevator pitch**, BioGenies. \n1. 11-08-2021: **Wstęp do wstępu do modeli liniowych**, Krystyna Grzesiak. \n1. 04-08-2021: **Is the human genome 3D structure an inherited trait?**, Michał Łaźniewski. \n1. 28-07-2021: **PlastoGram**, Katarzyna Sidorczuk.\n1. 21-07-2021: **How to eat ice cream?**, Dominik Rafacz.\n1. 14-07-2021: **BioGenies update #5: Year One**, Michał Burdukiewicz.\n1. 12-07-2021: **Computational modeling of protein-protein complexes with therapeutic binding proteins**, Filip Radom.\n1. 07-07-2021: **OpenPGX: a personalized approach to pharmacogenomics recommendations**, Monika Krzyżanowska.\n1. 30-06-2021: **Filtering k-mer matrices - master thesis**, Jakub Kała.\n1. 23-06-2021: Genomics Platform@WUT conference.\n1. 16-06-2021: **Comparing deuteration curves**, Krystyna Grzesiak.\n1. 09-06-2021: no seminar, only update.\n1. 02-06-2021: **Bioinformatic and experimental analyses of bacterial functional amyloids CsgA and CsgB**, Jarosław Chilimoniuk.\n1. 26-05-2021: **A3D 2.0 update for the prediction and optimization of protein solubility**, Jordi Pujols, Valentín Iglesias.\n1. 19-05-2021: **Comparing deuteration curves**, Krystyna Grzesiak.\n1. 12-05-2021: **LILO: a database of biological learners**, Michał Burdukiewicz.\n1. 05-05-2021: **Ocena jakości nadzorowanych metod uczenia klasyfikacji**, Katarzyna Stapor.\n1. 28-04-2021: **Comparing deuteration curves**, Krystyna Grzesiak.\n1. 21-04-2021: **ampir: an R package for fast genome-wide prediction of antimicrobial peptides**, Legana C H W Fingerhut, Ira Cooke.\n1. 14-04-2021: no seminar, only update.\n1. 07-04-2021: **Uncertainties in HDX-MS measurements**, Weronika Puchała.\n1. 31-03-2021: **BioGenies update #4**, Michał Burdukiewicz.\n1. 24-03-2021: **Improved metagenome binning and assembly using deep variational autoencoders**, Simon Rasmussen.\n1. 17-03-2021: **Filtering k-mer matrices - follow up**, Jakub Kała.\n1. 10-03-2021: **Filtering k-mer matrices**, Jakub Kała.\n1. 03-03-2021: **MegaGO: a fast yet powerful approach to assess functional gene ontology similarity across meta-omics data sets**, Henning Schiebenhöfer.\n1. 24-02-2021: **Deploying apps in shinyproxy on BioGenies web server**, Filip Pietluch.\n1. 17-02-2021: **Comparing deuteration curves**, Krystyna Grzesiak.\n1. 10-02-2021: **k-mer space as an efficient representation  of biological sequences**, Jadwiga Słowik.\n1. 03-02-2021: **Generation of negative datasets**, Michał Burdukiewicz.\n1. 27-01-2021: **Low complexity proteins**, Aleksandra Gruca.\n1. 20-01-2021: **Biology for data scientists**, Dominik Cysewski.\n1. 13-01-2021: **Bayesian optimization in prediction of amyloid proteins**, Paulina Grudzińska. ~~**Writing loops in R**, Mateusz Bąkała.~~\n1. 16-12-2020: **Podsumowanie roku**, BioGenies.\n1. 09-12-2020: **Frontiers of precision medicine**, Stefan Rödiger.\n1. 02-12-2020: **BioGenies update #3**, Michał Burdukiewicz.\n1. 25-11-2020: **High-resolution HDX - follow up**, Weronika Puchała.\n1. 18-11-2020: **High-resolution HDX**, Weronika Puchała.\n1. 04-11-2020: **BioGenies update #2**, Michał Burdukiewicz. ~~**Writing loops in R**, Mateusz Bąkała.~~ \n1. 28-10-2020: **tidysq - follow up**, Dominik Rafacz.\n1. 21-10-2020: **tidysq**, Dominik Rafacz.\n1. 14-10-2020: ~~**Frontiers of precision medicine**, Stefan Rödiger.~~\n1. 07-10-2020: **Simulating sequences for feature filtering - follow up**, Jakub Kała.\n1. 30-09-2020: **Simulating sequences for feature filtering**, Jakub Kała.\n1. 23-09-2020: Why R? presentations - general test.\n1. 16-09-2020: **BioGenies update #1**, Michał Burdukiewicz.\n1. 09-09-2020: **Evolution of AMPs**, Przemysław Gagat.\n1. 02-09-2020: **How to organise a project**, Leon Eyrich Jessen.\n1. 26-08-2020: **Using UniProt**, Filip Pietluch.\n1. 19-08-2020: **Proteomics 101, part 2**, Dominik Cysewski.\n1. 12-08-2020: **Proteomics 101, part 1**, Dominik Cysewski.\n1. 5-08-2020: **tidysq forum: o kopiach obiektów w R**, Mateusz Bąkała.\n1. 29-07-2020: **VisQual**, Jan Sawicki.\n1. 22-07-2020: **HaDeX**, Weronika Puchała.\n1. 15-07-2020: **AmpGram**, Katarzyna Sidorczuk.\n1. 8-07-2020: **QuiPT and feature filtering**, Jakub Kała.\n1. 1-07-2020: **Effective k-mer counting**, Jadwiga Słowik.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiogenies%2Fseminar","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiogenies%2Fseminar","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiogenies%2Fseminar/lists"}