diff --git a/_freeze/subsite/seminars/execute-results/html.json b/_freeze/subsite/seminars/execute-results/html.json index bf811d3..41aa11a 100644 --- a/_freeze/subsite/seminars/execute-results/html.json +++ b/_freeze/subsite/seminars/execute-results/html.json @@ -1,8 +1,8 @@ { - "hash": "70b9728adf8d5bb9ce63e94bbd35658d", + "hash": "a48eb2d14376c90c6bd6a8c53e2903db", "result": { "engine": "knitr", - "markdown": "---\ntitle: \"Seminars\"\n---\n\n\n**Are you interested to join our seminars or particular seminar? Just email us.**\n\n\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. 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. (maybe) 17-04-2023: **Introduction to metabolomics**, Michał Ciborowski (in Polish).\n1. 03-04-2023: **Preludium to science**, Jarosław Chilimoniuk & 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 & 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", + "markdown": "---\ntitle: \"Seminars\"\n---\n\n\n**Are you interested to join our seminars or particular seminar? Just email us.**\n\n\n1. 2024-08-26: **AmyloGraph 2.0 - project ideas**, Michał Burdukiewicz.\n 2. 2024-08-19: **Funny stories**, Weronika Puchała, Jakub Kołodziejczyk.\n 3. 2024-07-12: **BioGenies website ideas**, Jarek Chilimoniuk.\n 4. 2024-07-05: no seminar.\n 5. 2024-07-01: **Metabocrates**, Filip Gaj | **Pathway analysis tailored for metabolomic data**, Joanna Pokora.\n 6. 2024-06-24: no seminar.\n 7. 2024-06-17: **Miniatura grant**, Michał Burdukiewicz.\n 8. 2024-06-16: Long lack of planned seminars because Michał was traveling and other things.\n 9. 2024-01-08: **BioGenies in 2024**, Michał Burdukiewicz.\n 10. 2023-12-18: **THE SEMINAR**, Oriol Bárcenas.\n 11. 2023-11-20: **Robust dataset generation and feature characterization for the specific prediction and benchmarking of client and driver proteins in LLPS**, Carlos Pintado-Grima.\n 12. 2023-11-13: **Deep neural networks (Understanding Deep Learning, Chapter 8)**, Jakub Kała.\n 13. 2023-11-04: no seminar.\n 14. 2023-10-30: **BioGenies update #10**, Michal Burdukiewicz.\n 15. 2023-10-23: **Cracking the black box of deep sequence-based protein-protein interaction prediction**, Judith Bernett.\n 16. 2023-10-16: **Cracking the black box of deep sequence-based protein-protein interaction prediction (pre-print comments)**, Jarosław Chilimoniuk.\n 17. 2023-10-09: **Analysis of amyloid-amyloid interaction networks**, Laura Bąkała.\n 18. 2023-10-02: **Tree of science**, Michał Burdukiewicz.\n 19. 2023-09-25: **Deep neural networks (Understanding Deep Learning, Chapter 7)**, Jakub Kała.\n 20. 2023-09-18: **Symptome Checkers**, Michał Burdukiewicz.\n 21. 2023-09-11: **Deep neural networks (Understanding Deep Learning, Chapter 6)**, Jakub Kała.\n 22. 2023-08-21: **Copernican Revolution**, Michał Burdukiewicz.\n 23. 2023-08-18: **BioGenies: Year 3**.\n 24. 2023-08-14: no seminar, we move it to 18-08-2023.\n 25. 2023-08-07: **Deep neural networks (Understanding Deep Learning, Chapter 6)**, Jakub Kała.\n 26. 2023-07-31: **Deep neural networks (Understanding Deep Learning, Chapter 5): notebooks**, Jakub Kała.\n 27. 2023-07-17: **BioGenies update #9**, Michal Burdukiewicz.\n 28. 2023-07-10: **Deep neural networks (Understanding Deep Learning, Chapter 4): notebooks**, Michal Burdukiewicz.\n 29. 2023-07-03: **Styles with Benefits. The StyloMetrix Vectors for Stylistic and Semantic Text Classification of Small-Scale Datasets and Different Sample Length**, Inez Okulska.\n 30. 2023-06-26: **Shallow neural networks (Understanding Deep Learning, Chapter 3): notebooks**, Jakub Kała.\n 31. 2023-06-19: ~~**Shallow neural networks (Understanding Deep Learning, Chapter 3): notebooks**, Jakub Kała.~~ (Michał was not available)\n 32. 2023-06-12: **Shallow neural networks (Understanding Deep Learning, Chapter 3)**, Jakub Kała.\n 33. 2023-06-05: **Supervised learning (Understanding Deep Learning, Chapter 2)**, Michał Burdukiewicz.\n 34. 2023-05-19: **When quality does not matter: a curious case of the subplastid location prediction**, Michał Burdukiewicz\n 35. 2023-05-12: **Grantopisanie**, Michał Burdukiewicz.\n 36. 2023-04-17: **Introduction to metabolomics**, Michał Ciborowski (in Polish).\n 37. 2023-04-03: **Preludium to science**, Jarosław Chilimoniuk & Krystyna Grzesiak.\n 38. 2023-03-27: **Prediction of adhesins**, Katarzyna Sidorczuk.\n 39. 2023-03-20: **Imputomics**, Jarosław Chilimoniuk.\n 40. 2023-03-13: **Introduction to metabolomics**, Michał Ciborowski (in Polish).\n 41. 2023-03-06: \n 42. 2023-02-27: \n 43. 2023-02-20: **Mining the entire space of peptide sequences**, Michał Burdukiewicz and Jakub Kała.\n 44. 2023-02-13: **A heuristic algorithm solving the mutual-exclusivity sorting problem**, Alessandro Vinceti.\n 45. 2023-02-06: **Optimal ensemble selection, part 2**, Michał Burdukiewicz.\n 46. 2023-01-30: no seminar, only update.\n 47. 2023-01-23: **Optimal ensemble selection**, Michał Burdukiewicz.\n 48. 2023-01-16: **Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?**, Carlos Alberto Brizuela Rodríguez.\n 49. 2023-01-10: **BioGenies in 2023**.\n 50. 2022-12-12: ~~**Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?**, Carlos Alberto Brizuela Rodríguez.~~ only update.\n 51. 2022-12-05: **AMPLE: detection of antimicrobial peptides in metagenomic data** Michał Burdukiewicz.\n 52. 2022-11-28: **Lessons from Poland** Michał Burdukiewicz.\n 53. 2022-11-21: no seminar, Michał is still networking in Warsaw.\n 54. 2022-11-14: no seminar, Michał is networking in Warsaw.\n 55. 2022-11-07: no seminar, Michał is networking in Białystok.\n 56. 2022-10-31: **Your scariest research** BioGenies.\n 57. 2022-10-26: no seminar, Michał is networking in Wrocław.\n 58. 2022-10-17: **Pitfalls of machine learning for peptide analysis**, Michał Burdukiewicz.\n 59. 2022-10-10: **The dynamic landscape of peptide function prediction** Oriol Bárcenas, Michał Burdukiewicz, Carlos Pintado-Grima.\n 60. 2022-10-03: **BioGenies update #8**, Michał Burdukiewicz.\n 61. 2022-09-26: **DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides**, Heng Zheng (MS Teams).\n 62. 2022-09-19: no seminar, Michał has fun at the ECCB2022.\n 63. 2022-09-12: no seminar, Michał has fun at the Barcelona Aggregation Training School.\n 64. 2022-09-05: **Optimal prediction of antimicrobial peptides, part 2**, Michał Burdukiewicz.\n 65. 2022-08-29: **Optimal prediction of antimicrobial peptides**, Michał Burdukiewicz.\n 66. 2022-08-22: **PlastoGram v2**, Katarzyna Sidorczuk.\n 67. 2022-08-15: Public holidays.\n 68. 2022-08-08: **PlastoGram v1**, Katarzyna Sidorczuk.\n 69. 2022-08-02: **BioGenies update #7**, Michał Burdukiewicz.\n 70. 2022-07-25: **Empirical Bayes functional models for hydrogen deuterium exchange mass spectrometry**, Oliver M Crook.\n 71. 2022-07-18: **Transfer learning in proteins: evaluating novel protein learned representations for bioinformatics tasks**, Emilio Fenoy.\n 72. 2022-07-11: **Do deep learning models make a difference in the identification of antimicrobial peptides?**, Carlos Alberto Brizuela Rodríguez.\n 73. 2022-07-04: **Inside the web of science**, Michał Burdukiewicz.\n 74. 2022-06-27: **golem**, Dominik Rafacz & Gustav Meyrink.\n 75. 2022-06-20: **bookdown**, Krystyna Grzesiak.\n 76. 2022-06-13: no seminar, only update. \n 77. 2022-06-06: no seminar, only update.\n 78. 2022-05-30: **Zastosowania zautomatyzowanej kuracji jakości danych w modelowaniu systemów immunoinformatycznych opartym na uczeniu maszynowym**, Dominik Rafacz.\n 79. 2022-05-23: no seminar, only update.\n 80. 2022-05-16: **Modularizing Shiny**, Dominik Rafacz.\n 81. 2022-05-09: **Analiza wpływu czynników środowiskowych oraz zanieczyszczeńpowietrza na choroby układu otolaryngologicznego na podstawie kohorty wrocławskiej z 2015 roku**, Dominik Nowakowski\n 82. 2022-04-25: **Shiny intro**, Michał Burdukiewicz.\n 83. 2022-04-11: **Effective presentations**, Mariusz Trojanowski.\n 84. 2022-04-04: no seminar, only update.\n 85. 2022-03-28: **Peer-review principles**, Michał Burdukiewicz.\n 86. 2022-03-21: no seminar, only update.\n 87. 2022-03-14: no seminar, only update.\n 88. 2022-03-07: **Michał talks about things**, Michał Burdukiewicz.\n 89. 2022-03-02: no seminar, only update.\n 90. 2022-02-16: no seminar, only update.\n 91. 2022-02-09: no seminar, only update.\n 92. 2022-02-02: **AmyloGraph: Michał nie umie w zarządzanie**, Michał Burdukiewicz. \n 93. 2022-01-26: **protti: an R package for comprehensive data analysis of peptide- and protein-centric bottom-up proteomics data**, Jan-Philipp Quast. \n 94. 2022-01-19: **New Year's Resolutions**, Michał Burdukiewicz.\n 95. 2021-12-22: **Memomikołajki**, BioGenies.\n 96. 2021-12-15: **BioGenies update #6**, Michał Burdukiewicz.\n 97. 2021-12-08: **Molecular Insights into the Differential Dynamics of SARS-CoV-2 Variants of Concern (VOC)**, Nabanita Mandal.\n 98. 2021-12-01: **Applications of automated data quality curation in machine learning based modelling of immunoinformatic systems: Episode One**, Dominik Rafacz.\n 99. 2021-11-24: **adhesiomeR**, Katarzyna Sidorczuk.\n 100. 2021-11-17: **Peptipedia**, David Medina-Ortiz (new time: 3 PM UTC+2).\n 101. 2021-11-10: **Building HMM and molecular docking analysis for the sensitive detection of anti-viral pneumonia antimicrobial peptides (AMPs)**, Olalekan Bakare.\n 102. 2021-11-03: **Blood-brain barrier peptides**, Michał Burdukiewicz.\n 103. 2021-10-27: **LILOP 2.0: I am choosing my hair color**, Michał Burdukiewicz.\n 104. 2021-10-20: **Poster session at IBB**, BioGenies.\n 105. 2021-10-13: **My own github profile readme**, Michał Burdukiewicz.\n 106. 2021-10-06: **Protein-peptide docking in the era of accurate structure-prediction**, Sebastian Kmiecik.\n 107. 2021-09-29: **Why my research is bad?**, Michał Burdukiewicz. \n 108. 2021-09-22: no seminar, only update.\n 109. 2021-09-15: **AmyloGraph: a comprehensive database of amyloid-amyloid interactions**, Michał Burdukiewicz. \n 110. 2021-09-08: **Novel project managment**, Krystyna Grzesiak, Weronika Puchała.\n 111. 2021-09-01: **Wstęp do modeli liniowych**, Krystyna Grzesiak. \n 112. 2021-08-25: **Next grants**, Michał Burdukiewicz. \n 113. 2021-08-18: **Elevator pitch**, BioGenies. \n 114. 2021-08-11: **Wstęp do wstępu do modeli liniowych**, Krystyna Grzesiak. \n 115. 2021-08-04: **Is the human genome 3D structure an inherited trait?**, Michał Łaźniewski. \n 116. 2021-07-28: **PlastoGram**, Katarzyna Sidorczuk.\n 117. 2021-07-21: **How to eat ice cream?**, Dominik Rafacz.\n 118. 2021-07-14: **BioGenies update #5: Year One**, Michał Burdukiewicz.\n 119. 2021-07-12: **Computational modeling of protein-protein complexes with therapeutic binding proteins**, Filip Radom.\n 120. 2021-07-07: **OpenPGX: a personalized approach to pharmacogenomics recommendations**, Monika Krzyżanowska.\n 121. 2021-06-30: **Filtering k-mer matrices - master thesis**, Jakub Kała.\n 122. 2021-06-23: Genomics Platform@WUT conference.\n 123. 2021-06-16: **Comparing deuteration curves**, Krystyna Grzesiak.\n 124. 2021-06-09: no seminar, only update.\n 125. 2021-06-02: **Bioinformatic and experimental analyses of bacterial functional amyloids CsgA and CsgB**, Jarosław Chilimoniuk.\n 126. 2021-05-26: **A3D 2.0 update for the prediction and optimization of protein solubility**, Jordi Pujols, Valentín Iglesias.\n 127. 2021-05-19: **Comparing deuteration curves**, Krystyna Grzesiak.\n 128. 2021-05-12: **LILO: a database of biological learners**, Michał Burdukiewicz.\n 129. 2021-05-05: **Ocena jakości nadzorowanych metod uczenia klasyfikacji**, Katarzyna Stapor.\n 130. 2021-04-28: **Comparing deuteration curves**, Krystyna Grzesiak.\n 131. 2021-04-21: **ampir: an R package for fast genome-wide prediction of antimicrobial peptides**, Legana C H W Fingerhut, Ira Cooke.\n 132. 2021-04-14: no seminar, only update.\n 133. 2021-04-07: **Uncertainties in HDX-MS measurements**, Weronika Puchała.\n 134. 2021-03-31: **BioGenies update #4**, Michał Burdukiewicz.\n 135. 2021-03-24: **Improved metagenome binning and assembly using deep variational autoencoders**, Simon Rasmussen.\n 136. 2021-03-17: **Filtering k-mer matrices - follow up**, Jakub Kała.\n 137. 2021-03-10: **Filtering k-mer matrices**, Jakub Kała.\n 138. 2021-03-03: **MegaGO: a fast yet powerful approach to assess functional gene ontology similarity across meta-omics data sets**, Henning Schiebenhöfer.\n 139. 2021-02-24: **Deploying apps in shinyproxy on BioGenies web server**, Filip Pietluch.\n 140. 2021-02-17: **Comparing deuteration curves**, Krystyna Grzesiak.\n 141. 2021-02-10: **k-mer space as an efficient representation of biological sequences**, Jadwiga Słowik.\n 142. 2021-02-03: **Generation of negative datasets**, Michał Burdukiewicz.\n 143. 2021-01-27: **Low complexity proteins**, Aleksandra Gruca.\n 144. 2021-01-20: **Biology for data scientists**, Dominik Cysewski.\n 145. 2021-01-13: **Bayesian optimization in prediction of amyloid proteins**, Paulina Grudzińska. ~~**Writing loops in R**, Mateusz Bąkała.~~\n 146. 2020-12-16: **Podsumowanie roku**, BioGenies.\n 147. 2020-12-09: **Frontiers of precision medicine**, Stefan Rödiger.\n 148. 2020-12-02: **BioGenies update #3**, Michał Burdukiewicz.\n 149. 2020-11-25: **High-resolution HDX - follow up**, Weronika Puchała.\n 150. 2020-11-18: **High-resolution HDX**, Weronika Puchała.\n 151. 2020-11-04: **BioGenies update #2**, Michał Burdukiewicz. ~~**Writing loops in R**, Mateusz Bąkała.~~ \n 152. 2020-10-28: **tidysq - follow up**, Dominik Rafacz.\n 153. 2020-10-21: **tidysq**, Dominik Rafacz.\n 154. 2020-10-14: ~~**Frontiers of precision medicine**, Stefan Rödiger.~~\n 155. 2020-10-07: **Simulating sequences for feature filtering - follow up**, Jakub Kała.\n 156. 2020-09-30: **Simulating sequences for feature filtering**, Jakub Kała.\n 157. 2020-09-23: Why R? presentations - general test.\n 158. 2020-09-16: **BioGenies update #1**, Michał Burdukiewicz.\n 159. 2020-09-09: **Evolution of AMPs**, Przemysław Gagat.\n 160. 2020-09-02: **How to organise a project**, Leon Eyrich Jessen.\n 161. 2020-08-26: **Using UniProt**, Filip Pietluch.\n 162. 2020-08-19: **Proteomics 101, part 2**, Dominik Cysewski.\n 163. 2020-08-12: **Proteomics 101, part 1**, Dominik Cysewski.\n 164. 2020-08-05: **tidysq forum: o kopiach obiektów w R**, Mateusz Bąkała.\n 165. 2020-07-29: **VisQual**, Jan Sawicki.\n 166. 2020-07-22: **HaDeX**, Weronika Puchała.\n 167. 2020-07-15: **AmpGram**, Katarzyna Sidorczuk.\n 168. 2020-07-08: **QuiPT and feature filtering**, Jakub Kała.\n 169. 2020-07-01: **Effective k-mer counting**, Jadwiga Słowik.\n", "supporting": [], "filters": [ "rmarkdown/pagebreak.lua" diff --git a/subsite/alumni.qmd b/subsite/alumni.qmd index a68cce7..665f5d0 100644 --- a/subsite/alumni.qmd +++ b/subsite/alumni.qmd @@ -13,6 +13,8 @@ title: "Former Team Members" [![Anna Lassota](fig/temp_profile.png "temporary profile pic"){}]() +[![Dominik Nowakowski](fig/temp_profile.png "temporary profile pic"){}]() + [![Filip Pietluch](fig/temp_profile.png "temporary profile pic"){}]() [![Dominik Rafacz](fig/temp_profile.png "temporary profile pic"){}]() diff --git a/subsite/seminars.qmd b/subsite/seminars.qmd index e79a386..9861b78 100644 --- a/subsite/seminars.qmd +++ b/subsite/seminars.qmd @@ -5,16 +5,28 @@ title: "Seminars" **Are you interested to join our seminars or particular seminar? Just email us.** ```{r, results='asis', echo=FALSE, message=FALSE} +library(tidyverse) library(RCurl) URL <- "https://raw.githubusercontent.com/BioGenies/seminar/master/README.md" -#all_lines <- iconv(strsplit(getURL(URL), "\n")[[1]], from = "UTF-8", to = "UTF-8") -all_lines <- strsplit(getURL(URL, .encoding = "UTF-8"), "\n")[[1]] - - -cat(all_lines[-c(1, 2)], sep = "\n") - -# sem_df <- x %>% str_split(., "\n[0-9]+. ") %>% tibble() %>% unnest() %>% rename("id" = ".") %>% separate(., col = 'id', into = c("date", "title"), sep = ": ") +# all_lines <- iconv(strsplit(getURL(URL), "\n")[[1]], from = "UTF-8", to = "UTF-8") +seminar_lines <- strsplit(getURL(URL, .encoding = "UTF-8"), "\n")[[1]] #%>% as_tibble() + + +sem_df <- read_lines(URL)[-c(1:2)] %>% str_flatten() %>% + str_replace_all(., "\\d{1,3}\\.\\s", "21U37") %>% + str_split(., "21U37") %>% as_tibble(., .name_repair = "universal") %>% .[-1, ] %>% + separate(., col = "...1", into = c("date", "rest"), sep = ": ", extra = "merge") %>% + mutate(date = date %>% as.Date(., "%d-%m-%Y")) %>% + rowid_to_column(var = "no") %>% + mutate(rmarkdown = paste0(no, ". ", date, ": ", rest, "\n")) + +# #%>% +# separate(., col = value, into = c("date", "rest"), sep = ": ", extra = "merge") %>% +# separate(., col = rest, into = c("title", "presenting"), sep = "\\*, ", extra = "merge") %>% +# str_remove_all(., "^[0-9]+. ") %>% str_remove_all(., "\\n") %>% as_tibble() + +cat(sem_df$rmarkdown) # sem_df %>% DT::datatable()