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--- teaching:2020summer:compan [2020/04/17 17:43]
tischulz Moved free week and added some paper links.
+++ teaching:2020summer:compan [2020/06/10 11:57]
tischulz Added slides and link to latex beamer doku
@@ Line 5: / Line 5: @@
 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 =====
@@ Line 13: / Line 16: @@
 | 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.  | -- |                                               |
+| 17.06.  | presentations (1) |                                               |
-| 24.06.  | presentations (1) |                                                                                                                    |
+| 24.06.  | presentations (2) |                                                                                                                    |
-| 01.07.  | presentations (2) |   |
+| 01.07.  | presentations (3) |   |
-| 08.07.  | presentations (3) |  |
+| 08.07.  | presentations (4) |  |
-| 15.07.  | presentations (4) |  |
+| 15.07.  | presentations (5) |  |
@@ Line 36: / Line 39: @@
 ^ 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  | Yannick  | [[ 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://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 ]] |
+|  4  | Fabian  | [[ https://www.liebertpub.com/doi/pdfplus/10.1089/cmb.2019.0309 | Efficient Construction of a Complete Index for Pan-Genomics Read 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 ]] |
+|  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 ]] |
+|  5  | Christoph  | [[ https://www.biorxiv.org/content/10.1101/645721v1.full.pdf | Viral quasispecies reconstruction via contig abundance estimation in variation graphs ]] |
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Genome Informatics

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