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teaching:2020summer:compan [2020/04/21 14:12] tischulz Added more papers and another presentation slot |
teaching:2020summer:compan [2020/07/06 11:52] (current) tischulz Removed Yannick from schedule |
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| Office: U10-141\\ | Office: U10-141\\ | ||
| + | \\ | ||
| + | **Important notice:**\\ | ||
| + | The seminar will take place as an online course via Zoom. Details for participation can be found at the [[ https://bis.uni-bielefeld.de/sites/27608/Start.aspx | Lernraum ]]. | ||
| ===== Contents ===== | ===== Contents ===== | ||
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| | 22.04. | Preliminaries, topic selection | | | | 22.04. | Preliminaries, topic selection | | | ||
| - | | 29.04. | Intro to LaTeX, reading | | | + | | 29.04. | Intro to LaTeX, reading | {{ :teaching:2020summer:compan:template.tar | latex sources }}, {{ :teaching:2020summer:compan:reading.pdf | Slides: HowToRead }} | |
| - | | 06.05. | Scientific writing | | | + | | 06.05. | Scientific writing | {{ :teaching:2020summer:compan:scientificwriting.pdf | Slides: ScientificWriting }}, [[ https://de.sharelatex.com/learn/bibtex_bibliography_styles | Bibliography Styles ]] | |
| - | | 13.05. | Introductions, conclusions | | | + | | 13.05. | Introductions, conclusions | {{ :teaching:2020summer:compan:introsconclusions.pdf | Slides: IntroductionConclusions }} | |
| - | | 20.05. | Math | | | + | | 20.05. | Math | {{ :teaching:2020summer:compan:math_template.tar | latex sources }}, {{ :teaching:2020summer:compan:math.pdf | Slides: Math }} | |
| - | | 27.05. | Tables, figures, algorithms | | | + | | 27.05. | Tables, figures, algorithms | {{ :teaching:2020summer:compan:algo_template.tar | latex sources }}, {{ :teaching:2020summer:compan:tablesFiguresAlgos.pdf | Slides: TablesFiguresAlgorithms }} | |
| - | | 03.06. | Checklist, writing | | | + | | 03.06. | Checklist, writing | {{ :teaching:2020summer:compan:checklist.pdf | Slides: Checklist }} | |
| - | | 10.06. | Intro to presentations (in LaTeX Beamer) | | | + | | 10.06. | Intro to presentations (in LaTeX Beamer) | {{:teaching:2020summer:compan:beamer_template.tar | latex sources }}, [[ http://texdoc.net/texmf-dist/doc/latex/beamer/beameruserguide.pdf | beamer class doku ]], {{:teaching:2020summer:compan:checklist_presentations.pdf | Slides: Presentation Checklist }} | |
| | 17.06. | presentations (1) | | | | 17.06. | presentations (1) | | | ||
| | 24.06. | presentations (2) | | | | 24.06. | presentations (2) | | | ||
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| ^ Slot ^ Student ^ Paper ^ | ^ Slot ^ Student ^ Paper ^ | ||
| - | | | | [[ https://watermark.silverchair.com/bbw089.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAmkwggJlBgkqhkiG9w0BBwagggJWMIICUgIBADCCAksGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMZGJ4Sz-sg9kIaVEyAgEQgIICHMkoibfrcZ3sD66-CDQolNZcEHVhrur0KAluNvo-s8T8Z9Do_YhXSPgYRN-AgRdWWN1tbyOBJ8hUoh8CwXJbKzg7irXbJtI8oInBgaHVScIwN2Ln2TgtmLkdEFU9SYdek6mNI-x7S7fd6bDzQXFqSl1SjHJvatvmy9QtPTcMDKQCuB7eVJNKemAgrIXSKMaNFQcx9BDZDGY1Xnb0O4zawf5UamzRY02xeCzJV2o56TNebfpu87Ou2xSXgil9QjQsjxsV60Uj3LdgC6km6Ml2cOq7SCL3ufewR84nAAPdpEFwQXmqGg23p_8D0pEHIEXZlzVwIW49JRyU_Sm83f5785FCZAhxILCmPJdrTptu3CZRI3TpUfEOVB00TospZhzlF4mf_C8XtXI1QB8zqNdiUzH-93GbX0rf8I_O6aKCrZEvsv5ohvyIlb3KS5PFFAyxxue4JMh8Lmslq6jl95KHvGWGt1lRuEWzJkZaHEGuI8tcPib1pcliwlBrLK4o34uiytqVVo6Ir2fw88rZVALKQk3GFh8T0Bc8DmxzFYzMXwgHTu4k7wTmouMGGT5cugM96donLJg4y336yUgQjD4tnjrQ-4UJL88cZ-Vu1nKdE_bkP3M4nFPk3mzcTfhLJtMuia2ZJdyM66yq5U0f4lvv2AGSwcHmo0yriED-FQRyzvAh94xnE8P6KNqWZVN8yGLXYkF5nQKGnag9gf4cwA | Computational pan-genomics: status, promises and challenges ]] | | + | | 2 | Tizian | {{ :teaching:2020summer:compan:bbw089.pdf | Computational pan-genomics: status, promises and challenges }} | |
| - | | | | [[ https://almob.biomedcentral.com/track/pdf/10.1186/s13015-016-0066-8 | Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage ]] | | + | | | | [[ https://almob.biomedcentral.com/track/pdf/10.1186/s13015-016-0066-8 | Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage ]] | |
| - | | | | [[ https://www.biorxiv.org/content/10.1101/695338v2.full.pdf | Bifrost - Highly parallel construction and indexing of colored and compacted de Bruijn graphs ]] | | + | | 3 | <del>Yannick</del> | [[ https://www.biorxiv.org/content/10.1101/695338v2.full.pdf | Bifrost - Highly parallel construction and indexing of colored and compacted de Bruijn graphs ]] | |
| - | | | | [[ https://www.biorxiv.org/content/10.1101/234856v1.full.pdf | Sequence variation aware genome references and read mapping with the variation graph toolkit ]] | | + | | 3 | Marvin | [[ https://www.biorxiv.org/content/10.1101/234856v1.full.pdf | Sequence variation aware genome references and read mapping with the variation graph toolkit ]] | |
| - | | | | [[ https://www.liebertpub.com/doi/pdfplus/10.1089/cmb.2019.0309 | Efficient Construction of a Complete Index for Pan-Genomics Read Alignment ]] | | + | | 4 | Fabian | [[ https://www.liebertpub.com/doi/pdfplus/10.1089/cmb.2019.0309 | Efficient Construction of a Complete Index for Pan-Genomics Read Alignment ]] | |
| - | | | | [[ https://watermark.silverchair.com/btz162.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAApUwggKRBgkqhkiG9w0BBwagggKCMIICfgIBADCCAncGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMUPzoUo8feAPYcgwcAgEQgIICSM15_mSi3xEtbS7iYr7bUrDXEPAomor_yjOC2VIhuotTlEm0XJ46-YnneDqhz9_ZCdd1QFRAvzVhhr1jko0wfO8TV5K61ChH9n2IazdHRDJy3_MUc0fF5MKie_31bDMJXGXqKICZVHPRL8LT9clnG6qpRigT8baX2lDL8MyfACQyulTgIA1pb8nBQzKCBGRPBbrpcRNYtxX1qbFFj60-vBDDYNlgoJHLZzznUbYfS06Lv0qgmZuuzTh2BfEzwzQLpFJJRowP0RBwTvz9sq-95vK34h8I2VEbpiEh9NkpLcBTXfXe8VInUMkQXOPDDHvDLqnFLM8-XTS1wrwTocFCUQ6x1eAw9gLpkQjUB5wEMcJf4BwMvuNWMnuQbfw4-WFnGLdQa4v46GXs-5LRDV891fN3o7qVKMI_rGfuQPgrJq2ak5EqF_4wfmzzYZ5FXUWXP48vQlaATxGGuEtkRn5P-bniheIUOKA4hZE9sto9M8ziF7BE15VeS3uhyH4Ie-gkexL9_IOdkcgndTjfhi3YFDxUN9ozDXIQ81beyrkD4ZPAe6exnDTkVcSk5aqY1sRljg8giVKCDIC0fKcZIYGtEGYYme8LkSmHclMVWrAkJNUjirDtJ66C6hCxAX4CJpspjsYAIgNkkGtzmK-dtC6DRakoMhbFw6gfuqweUjjvplbFXP2Lrh8pTuvG74K3J_efU09B5hEbO_llWd6EQsMcm_Olok0RF06XIfTGvbcGGPqQPgbVYACyDa7A9SfcCSaS34aSgurtqZD2 | Bit-parallel sequence-to-graph alignment ]] | | + | | 5 | Leonard | [[ https://academic.oup.com/bioinformatics/article/35/19/3599/5372677 | Bit-parallel sequence-to-graph alignment ]] | |
| | | | [[ https://www.biorxiv.org/content/10.1101/2020.01.21.914168v1.full.pdf | BlastFrost: Fast querying of 100,000s of bacterial genomes in Bifrost graphs ]] | | | | | [[ https://www.biorxiv.org/content/10.1101/2020.01.21.914168v1.full.pdf | BlastFrost: Fast querying of 100,000s of bacterial genomes in Bifrost graphs ]] | | ||
| - | | | | [[ https://link.springer.com/content/pdf/10.1186/s13015-020-00164-3.pdf | Alignment- and reference-free phylogenomics with colored de Bruijn graphs ]] | | + | | 4 | Aya | [[ https://link.springer.com/content/pdf/10.1186/s13015-020-00164-3.pdf | Alignment- and reference-free phylogenomics with colored de Bruijn graphs ]] | |
| - | | | | [[ https://www.biorxiv.org/content/10.1101/645721v1.full.pdf | Viral quasispecies reconstruction via contig abundance estimation in variation graphs ]] | | + | | 5 | Christoph | [[ https://www.biorxiv.org/content/10.1101/645721v1.full.pdf | Viral quasispecies reconstruction via contig abundance estimation in variation graphs ]] | |
| Back to [[:teaching|Teaching]] | Back to [[:teaching|Teaching]] | ||
teaching/2020summer/compan.1587471158.txt.gz · Last modified: 2020/04/21 14:12 by tischulz
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