Add new tutorial for deciphering viral populations using SNV and baculovirus isolates (Variant analysis)

CONTRIBUTORS.yaml

@@ -1148,6 +1148,17 @@ jfallmann:
     name: Joerg Fallmann
     joined: 2017-09
 
+wennj:
+    name: Jörg Wennmann
+    email: [email protected]
+    orcid: 0000-0003-3060-8992
+    contact_for_training: true
+    joined: 2025-01
+    location:
+      country: DE
+      lat: 49.449466
+      lon: 8.640339
+
 jfaulon:
     name: Jean-Loup Faulon
     email: [email protected]

Gemfile.lock

@@ -1,21 +1,24 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    addressable (2.8.5)
-      public_suffix (>= 2.0.2, < 6.0)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
     awesome_bot (1.20.0)
       parallel (= 1.20.1)
-    bibtex-ruby (6.0.0)
+    bibtex-ruby (6.1.0)
       latex-decode (~> 0.0)
+      racc (~> 1.7)
+    bigdecimal (3.1.9)
     citeproc (1.0.10)
       namae (~> 1.0)
-    citeproc-ruby (2.0.0)
+    citeproc-ruby (2.1.0)
       citeproc (~> 1.0, >= 1.0.9)
       csl (~> 2.0)
+      observer (< 1.0)
     colorator (1.1.0)
-    commander (4.6.0)
-      highline (~> 2.0.0)
-    concurrent-ruby (1.2.2)
+    commander (5.0.0)
+      highline (~> 3.0.0)
+    concurrent-ruby (1.3.5)
     csl (2.0.0)
       namae (~> 1.0)
       rexml
@@ -28,12 +31,32 @@ GEM
     ethon (0.16.0)
       ffi (>= 1.15.0)
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-    fastimage (2.2.7)
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+    fastimage (2.4.0)
+    ffi (1.17.1-aarch64-linux-gnu)
+    ffi (1.17.1-aarch64-linux-musl)
+    ffi (1.17.1-arm-linux-gnu)
+    ffi (1.17.1-arm-linux-musl)
+    ffi (1.17.1-arm64-darwin)
+    ffi (1.17.1-x86_64-darwin)
+    ffi (1.17.1-x86_64-linux-gnu)
+    ffi (1.17.1-x86_64-linux-musl)
     forwardable-extended (2.6.0)
-    google-protobuf (3.25.5-x86_64-darwin)
-    google-protobuf (3.25.5-x86_64-linux)
-    highline (2.0.3)
+    google-protobuf (4.29.3)
+      bigdecimal
+      rake (>= 13)
+    google-protobuf (4.29.3-aarch64-linux)
+      bigdecimal
+      rake (>= 13)
+    google-protobuf (4.29.3-arm64-darwin)
+      bigdecimal
+      rake (>= 13)
+    google-protobuf (4.29.3-x86_64-darwin)
+      bigdecimal
+      rake (>= 13)
+    google-protobuf (4.29.3-x86_64-linux)
+      bigdecimal
+      rake (>= 13)
+    highline (3.0.1)
     html-proofer (4.4.3)
       addressable (~> 2.3)
       mercenary (~> 0.3)
@@ -44,9 +67,9 @@ GEM
       yell (~> 2.0)
       zeitwerk (~> 2.5)
     http_parser.rb (0.8.0)
-    i18n (1.14.1)
+    i18n (1.14.6)
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-    jekyll (4.3.2)
+    jekyll (4.3.4)
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       colorator (~> 1.0)
       em-websocket (~> 0.5)
@@ -70,59 +93,96 @@ GEM
       sass-embedded (~> 1.54)
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       listen (~> 3.0)
-    kramdown (2.4.0)
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+      rexml (>= 3.3.9)
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       kramdown (~> 2.0)
     kwalify (0.7.2)
     latex-decode (0.4.0)
     liquid (4.0.4)
-    listen (3.8.0)
+    listen (3.9.0)
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       rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.4.0)
-    namae (1.1.1)
-    nokogiri (1.16.5-x86_64-darwin)
+    namae (1.2.0)
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       date
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+    racc (1.8.1)
     rainbow (3.1.1)
+    rake (13.2.1)
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-    rb-inotify (0.10.1)
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+    rouge (4.5.1)
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-      google-protobuf (~> 3.23)
-    sass-embedded (1.69.5-x86_64-linux-gnu)
-      google-protobuf (~> 3.23)
+    sass-embedded (1.83.4-aarch64-linux-gnu)
+      google-protobuf (~> 4.29)
+    sass-embedded (1.83.4-aarch64-linux-musl)
+      google-protobuf (~> 4.29)
+    sass-embedded (1.83.4-arm-linux-gnueabihf)
+      google-protobuf (~> 4.29)
+    sass-embedded (1.83.4-arm-linux-musleabihf)
+      google-protobuf (~> 4.29)
+    sass-embedded (1.83.4-arm64-darwin)
+      google-protobuf (~> 4.29)
+    sass-embedded (1.83.4-x86_64-darwin)
+      google-protobuf (~> 4.29)
+    sass-embedded (1.83.4-x86_64-linux-gnu)
+      google-protobuf (~> 4.29)
+    sass-embedded (1.83.4-x86_64-linux-musl)
+      google-protobuf (~> 4.29)
     stringio (3.1.2)
     terminal-table (3.0.2)
       unicode-display_width (>= 1.1.1, < 3)
-    typhoeus (1.4.0)
+    typhoeus (1.4.1)
       ethon (>= 0.9.0)
-    unicode-display_width (2.5.0)
-    webrick (1.8.2)
+    unicode-display_width (2.6.0)
+    webrick (1.9.1)
     yell (2.2.2)
-    zeitwerk (2.6.12)
+    zeitwerk (2.7.1)
 
 PLATFORMS
-  x86_64-darwin-19
+  aarch64-linux
+  aarch64-linux-gnu
+  aarch64-linux-musl
+  arm-linux-gnu
+  arm-linux-gnueabihf
+  arm-linux-musl
+  arm-linux-musleabihf
+  arm64-darwin
+  x86_64-darwin
   x86_64-linux
+  x86_64-linux-gnu
+  x86_64-linux-musl
 
 DEPENDENCIES
   addressable
@@ -145,4 +205,4 @@ DEPENDENCIES
   webrick
 
 BUNDLED WITH
-   2.4.20
+   2.6.2

topics/variant-analysis/tutorials/baculovirus-isolate-variation/faqs/index.md

@@ -0,0 +1,3 @@
+---
+layout: faq-page
+---

topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.bib

@@ -0,0 +1,164 @@
+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+
+@article{Ayres1994,
+  title = {The Complete DNA Sequence of Autographa californica Nuclear Polyhedrosis Virus},
+  volume = {202},
+  ISSN = {0042-6822},
+  url = {http://dx.doi.org/10.1006/viro.1994.1380},
+  DOI = {10.1006/viro.1994.1380},
+  number = {2},
+  journal = {Virology},
+  publisher = {Elsevier BV},
+  author = {Ayres,  Martin D. and Howard,  Stephen C. and Kuzio,  John and Lopez-Ferber,  Miguel and Possee,  Robert D.},
+  year = {1994},
+  month = aug,
+  pages = {586–605}
+}
+
+@article{Cox2021,
+  title = {Innovations in the Insect Cell Expression System for Industrial Recombinant Vaccine Antigen Production},
+  volume = {9},
+  ISSN = {2076-393X},
+  url = {http://dx.doi.org/10.3390/vaccines9121504},
+  DOI = {10.3390/vaccines9121504},
+  number = {12},
+  journal = {Vaccines},
+  publisher = {MDPI AG},
+  author = {Cox,  Manon M. J.},
+  year = {2021},
+  month = dec,
+  pages = {1504}
+}
+
+@article{Fan2020,
+  title = {Population structure of Cydia pomonella granulovirus isolates revealed by quantitative analysis of genetic variation},
+  volume = {7},
+  ISSN = {2057-1577},
+  url = {http://dx.doi.org/10.1093/ve/veaa073},
+  DOI = {10.1093/ve/veaa073},
+  number = {1},
+  journal = {Virus Evolution},
+  publisher = {Oxford University Press (OUP)},
+  author = {Fan,  Jiangbin and Jehle,  Johannes A and Wennmann,  J\"{o}rg T},
+  year = {2020},
+  month = sep 
+}
+
+@article{Harrison2018,
+  title = {ICTV Virus Taxonomy Profile: Baculoviridae},
+  volume = {99},
+  ISSN = {1465-2099},
+  url = {http://dx.doi.org/10.1099/jgv.0.001107},
+  DOI = {10.1099/jgv.0.001107},
+  number = {9},
+  journal = {Journal of General Virology},
+  publisher = {Microbiology Society},
+  author = {Harrison,  Robert L. and Herniou,  Elisabeth A. and Jehle,  Johannes A. and Theilmann,  David A. and Burand,  John P. and Becnel,  James J. and Krell,  Peter J. and van Oers,  Monique M. and Mowery,  Joseph D. and Bauchan,  Gary R.},
+  year = {2018},
+  month = sep,
+  pages = {1185–1186}
+}
+
+@article{RodrguezHernndez2023,
+  title = {Baculovirus Display of Peptides and Proteins for Medical Applications},
+  volume = {15},
+  ISSN = {1999-4915},
+  url = {http://dx.doi.org/10.3390/v15020411},
+  DOI = {10.3390/v15020411},
+  number = {2},
+  journal = {Viruses},
+  publisher = {MDPI AG},
+  author = {Rodríguez-Hernández,  Aaron Pavel and Martínez-Flores,  Daniel and Cruz-Reséndiz,  Adolfo and Padilla-Flores,  Teresa and González-Flores,  Rodrigo and Estrada,  Kenia and Sampieri,  Alicia and Camacho-Zarco,  Aldo Román and Vaca,  Luis},
+  year = {2023},
+  month = feb,
+  pages = {411}
+}
+
+@article{vanOers2011,
+  title = {Opportunities and challenges for the baculovirus expression system},
+  volume = {107},
+  ISSN = {0022-2011},
+  url = {http://dx.doi.org/10.1016/j.jip.2011.05.001},
+  DOI = {10.1016/j.jip.2011.05.001},
+  journal = {Journal of Invertebrate Pathology},
+  publisher = {Elsevier BV},
+  author = {van Oers,  Monique M.},
+  year = {2011},
+  month = jul,
+  pages = {S3–S15}
+}
+
+@article{Wennmann2020,
+  title = {Bacsnp: Using Single Nucleotide Polymorphism (SNP) Specificities and Frequencies to Identify Genotype Composition in Baculoviruses},
+  volume = {12},
+  ISSN = {1999-4915},
+  url = {http://dx.doi.org/10.3390/v12060625},
+  DOI = {10.3390/v12060625},
+  number = {6},
+  journal = {Viruses},
+  publisher = {MDPI AG},
+  author = {Wennmann,  J\"{o}rg T. and Fan,  Jiangbin and Jehle,  Johannes A.},
+  year = {2020},
+  month = jun,
+  pages = {625}
+}
+
+@article{Wennmann2024,
+  title = {Haplotype determination of the Bombyx mori nucleopolyhedrovirus by Nanopore sequencing and linkage of single nucleotide variants},
+  volume = {105},
+  ISSN = {1465-2099},
+  url = {http://dx.doi.org/10.1099/jgv.0.001983},
+  DOI = {10.1099/jgv.0.001983},
+  number = {5},
+  journal = {Journal of General Virology},
+  publisher = {Microbiology Society},
+  author = {Wennmann,  J\"{o}rg T. and Lim,  Fang-Shiang and Senger,  Sergei and Gani,  Mudasir and Jehle,  Johannes A. and Keilwagen,  Jens},
+  year = {2024},
+  month = may 
+}
+
+@inbook{Eberle2012,
+  title = {Microbial control of crop pests using insect viruses.},
+  ISBN = {9781780640020},
+  url = {http://dx.doi.org/10.1079/9781845938086.0281},
+  DOI = {10.1079/9781845938086.0281},
+  booktitle = {Integrated pest management: principles and practice},
+  publisher = {CABI},
+  author = {Eberle,  K. E. and Jehle,  J. A. and Huber,  J.},
+  year = {2012},
+  month = jan,
+  pages = {281–298}
+}
+
+@inbook{Grzywacz2017,
+  title = {Production,  Formulation,  and Bioassay of Baculoviruses for Pest Control},
+  ISBN = {9780128035276},
+  url = {http://dx.doi.org/10.1016/B978-0-12-803527-6.00007-X},
+  DOI = {10.1016/b978-0-12-803527-6.00007-x},
+  booktitle = {Microbial Control of Insect and Mite Pests},
+  publisher = {Elsevier},
+  author = {Grzywacz,  D. and Moore,  S.},
+  year = {2017},
+  pages = {109–124}
+}
+
+@misc{ICTV_AcMNPV_genome_figure,
+  author = {International Committee on Taxonomy of Viruses (ICTV)},
+  title = {Genome mag of Autographa californica multiple nucleopolyhedrovirus isolate C6 (Figure 2)},
+  url = {\url{https://ictv.global/sites/default/files/inline-images/7651.ODD.Baculo.Fig2.v2.png}},
+  urldate = {2024-12-27}
+}