13 |
--------------------------------------------------------------------------------
/docs/tags/index.xml:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 | Tags on BioC Asia 2021
5 | /tags/
6 | Recent content in Tags on BioC Asia 2021
7 | Hugo -- gohugo.io
8 | en-us
9 |
10 |
11 |
--------------------------------------------------------------------------------
/docs/categories/index.xml:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 | Categories on BioC Asia 2021
5 | /categories/
6 | Recent content in Categories on BioC Asia 2021
7 | Hugo -- gohugo.io
8 | en-us
9 |
10 |
11 |
--------------------------------------------------------------------------------
/data/speakers/91.yaml:
--------------------------------------------------------------------------------
1 | text: "Erqiang Hu and Tizanzhi Wu are PhD students at the Department of Bioinformatics, Southern Medical University. The professor Guangchuang Yu group, including Erqiang and Tianzhi, recently published a paper on clusterProfiler 4.0 from the Innovation Journal. https://doi.org/10.1016/j.xinn.2021.100141"
2 | name: "Invited talk (day3 14:00~), Erqiang Hu and Tizanzhi Wu: \"clusterProfiler 4.0 and the new features\""
3 | position: "Southern Medical University, China"
4 | avatar: "img/speakers/ErqiangAndTizanzhi.png"
5 |
--------------------------------------------------------------------------------
/content/jobs.md:
--------------------------------------------------------------------------------
1 | +++
2 | title = "link to recruiting platform 'tayo'"
3 | description = "求人プラットフォーム tayo へのリンク"
4 | +++
5 |
6 | Here is a link to the recruiting platform called "tayo" for Japanese graduate students and researchers.
7 | Since "tayo" is currently focused on Japan, we will only introduce it in Japanese.
8 |
9 | 本ページでは大学院生や研究者に向けた、求人プラットフォーム tayo へのリンクを掲載します。
10 |
11 | ### **[tayo.jp](https://tayo.jp/)**
12 |
13 | 研究分野の求人情報にご興味をお持ちの方はぜひ御覧ください。
14 |
15 | [](https://tayo.jp/)
16 |
--------------------------------------------------------------------------------
/themes/hugo-universal-theme/.travis.yml:
--------------------------------------------------------------------------------
1 | sudo: required
2 | os:
3 | - osx
4 | language: ruby
5 | rvm:
6 | - 2.6.3
7 | env:
8 | - TRAVIS_NODE_VERSION="12"
9 | install:
10 | - rm -rf ~/.nvm && git clone https://github.com/creationix/nvm.git ~/.nvm && (cd ~/.nvm && git checkout `git describe --abbrev=0 --tags`) && source ~/.nvm/nvm.sh && nvm install $TRAVIS_NODE_VERSION
11 | - npm install
12 | - npm run install_hugo
13 | script:
14 | - npm run lint
15 | - cd exampleSite
16 | - hugo
17 | notifications:
18 | slack:
19 | rooms:
20 | - devcows:Qs59B9IYFi3IfrejVqNlN5G7#general
21 |
--------------------------------------------------------------------------------
/data/speakers/5.yaml:
--------------------------------------------------------------------------------
1 | text: "Nitesh Turaga is a core team member at the Bioconductor project, working at the intersection of Data Science, Computational biology, and Software Engineering. He is currently a Scientist in the Department of Data Science at Dana Farber Cancer Institute / Harvard. Before Bioconductor, he worked as a Software Engineer for the Galaxy Project at Johns Hopkins."
2 | name: "Invited talk (day2 13:30~), Nitesh Turaga: \"Efficient use of Bioconductor in cloud computing environment\""
3 | position: "Dana Farber Cancer Institute of Harvard Medical School, USA"
4 | avatar: "img/speakers/NiteshTuraga.jpeg"
5 |
--------------------------------------------------------------------------------
/data/speakers/6.yaml:
--------------------------------------------------------------------------------
1 | text: "Yunshun Chen is a senior postdoctoral researcher at Walter and Eliza Hall Institute of Medical Research. He is one of the authors and the main maintainer of the edgeR package - the arguably world’s most popular R package specifically designed for Next Generation Sequencing (NGS) data. His research focuses on differential expression analysis of the NGS data, as well as single-cell RNA-seq analysis."
2 | name: "Invited talk (day2 14:00~), Yunshun Chen: \"edgeR: differential analysis of sequence read count data\""
3 | position: "Walter and Eliza Hall Institute of Medical Research, Australia"
4 | avatar: "img/speakers/Andy.png"
5 |
--------------------------------------------------------------------------------
/themes/hugo-universal-theme/layouts/partials/top.html:
--------------------------------------------------------------------------------
1 | {{ if .Site.Params.topbar.enable }}
2 |
3 |
4 |
5 |
6 |
7 | {{ .Site.Params.topbar.text | safeHTML }}
8 |
9 |
10 |
11 | {{ range .Site.Menus.topbar.ByWeight }}
12 | {{ .Pre }}
13 | {{ end }}
14 |
15 |
16 |
17 |
18 |
19 |
20 | {{ end }}
21 |
--------------------------------------------------------------------------------
/data/speakers/9.yaml:
--------------------------------------------------------------------------------
1 | text: "Janani Ravi is an Assistant Professor in the Dept. of Pathobiology and Diagnostic Investigation at Michigan State University. Her research group develops computational approaches to study infectious diseases. Specific areas of their interest include protein sequence-structure-function relationships, comparative genomics, and drug repurposing. Janani is also the founder of two organizations that promote diversity in data science: R-Ladies East Lansing and Women+ Data Science."
2 | name: "Invited talk (day3 13:30~), Janani Ravi: \"AsiaR community and R-Ladies in Asia\""
3 | position: "Michigan State University, USA"
4 | avatar: "img/speakers/JananiRavi.jpeg"
5 |
--------------------------------------------------------------------------------
/data/speakers/92.yaml:
--------------------------------------------------------------------------------
1 | text: "Dr. Koki Tsuyuzaki is a post-doc researcher at RIKEN BDR BiT and a researcher at JST PRESTO. He is one of the active Bioconductor committers and has developed hundreds of R/Bioconductor packages including metaSeq, AHMeSHDbs, MeSHDbi, AHLRBaseDbs, LRBaseDbi, AHPubMedDbs, scTensor, and scTGIF. He will present his recent development of some R packages for tensor decomposition to handle large-scale and complex tensor data structures."
2 | name: "Invited talk (day3 14:30~), Koki Tsuyuzaki: \"Guidelines to handle large-scale and complex tensor data in R\""
3 | position: "RIKEN Center for Biosystems Dynamics Research, Japan"
4 | avatar: "img/speakers/KokiTsuyuzaki.jpg"
5 |
--------------------------------------------------------------------------------
/data/speakers/95.yaml:
--------------------------------------------------------------------------------
1 | text: "Shian Su is a PhD candidate at The Walter and Eliza Hall Institute of Medical Research. He is a maintainer of \"Glimma\" that accepts and visualizes differential expression results from \"limma\" and others https://doi.org/10.1093/bioinformatics/btx094 . He and Hasaru Kariyawasam recently published a preprint of Glimma 2.0 that enables interactive dashboard-style visualization in R Markdown https://doi.org/10.1101/2021.07.30.454464 ."
2 | name: "Invited talk (day4 14:30~), Shian Su: \"Dashboard-style interactive plots for RNA-seq analysis are R Markdown ready with Glimma 2.0\""
3 | position: "Walter and Eliza Hall Institute of Medical Research, Australia"
4 | avatar: "img/speakers/Shian.jpg"
5 |
--------------------------------------------------------------------------------
/themes/hugo-universal-theme/theme.toml:
--------------------------------------------------------------------------------
1 | name = "Universal"
2 | license = "MIT"
3 | licenselink = "https://github.com/devcows/hugo-universal-theme/blob/master/LICENSE"
4 | description = "A port of the Universal theme"
5 | homepage = "//github.com/devcows/hugo-universal-theme"
6 | tags = ["blog", "company", "portfolio", "projects", "minimal", "responsive"]
7 | features = ["blog", "themes", "disqus", "minimal", "responsive"]
8 | min_version = 0.15
9 |
10 | [author]
11 | name = "adrianmo"
12 | homepage = "//github.com/adrianmo"
13 |
14 | # If Porting existing theme
15 | [original]
16 | author = "bootstrapious"
17 | homepage = "http://bootstrapious.com/p/universal-business-e-commerce-template"
18 |
--------------------------------------------------------------------------------
/content/schedule.md:
--------------------------------------------------------------------------------
1 | +++
2 | title = "Schedule"
3 | description = "Schedule"
4 | +++
5 |
6 | # Schedule
7 |
8 | ### [All invited talk abstracts](https://biocasia2021.bioconductor.org/)
9 |
10 | ### [All contributed talk abstracts](https://biocasia2021.bioconductor.org/contributions/)
11 |
12 | ### [All workshop abstracts](https://biocasia2021.bioconductor.org/workshops/)
13 |
14 | Click or change **the place name in the left of "Powered by team up"** (in the lower-right corner) to set your time zone.
15 |
16 | You can also switch the calendar view from weekly view to **agenda view**.
17 | You can switch between them with **the button on the left of the hamburger menu** at the top right of the calendar.
18 |
19 | {{< iframe >}}
20 |
--------------------------------------------------------------------------------
/data/speakers/8.yaml:
--------------------------------------------------------------------------------
1 | text: "Dr Tatsuya Amano is an Australian Research Council Future Fellow at the School of Biological Sciences, the University of Queensland in Australia. He specializes in \"Conservation Science\" and launched a project to understand the consequences of the language barrier in biodiversity conservation (the translatE project – Transcending Language Barriers to Environmental Sciences: https://translatesciences.com). He also recently published an article called \"Ten tips for overcoming language barriers in science\". https://rdcu.be/cnZQf "
2 | name: "Keynote (day3 13:00~), Tatsuya Amano: \"Overcoming language barriers in science\""
3 | position: "The University of Queensland, Australia"
4 | avatar: "img/speakers/TatsuyaAmano.jpeg"
5 |
--------------------------------------------------------------------------------
/data/speakers/94.yaml:
--------------------------------------------------------------------------------
1 | text: "Hao (Harry) Feng is an Assistant Professor in the Department of Population and Quantitative Health Sciences at Case Western Reserve University. He is a biostatistician and bioinformatician by training. He is one of the authors and maintainers of the DSS package --- a method known for differential analysis in transcriptome and methylation sequencing data. His group develops statistical methods for high-throughput -omics data, especially in epigenomics and single-cell research. "
2 | name: "Invited talk (day4 14:00~), Hao Harry Feng: \"NeuCA: a neural network-based method for exhaustive cell label assignment using single cell RNA-seq data\""
3 | position: "Case Western Reserve University, USA"
4 | avatar: "img/speakers/feng-hao-harry.jpeg"
5 |
--------------------------------------------------------------------------------
/data/speakers/4.yaml:
--------------------------------------------------------------------------------
1 | text: "Lori Ann Shepherd is one of the members of the Bioconductor Core Team, Bioconductor Community Advisory Board and Bioconductor Technical Advisory Board. Since joining the core team, she has long designed and maintained Bioconductor key infrastructure and packages, administrated the package review process for package submissions from the community, and assisted with numerous courses, workshops, and conferences. Her efforts and contributions were recognized by being one of the 2020 inaugural Bioconductor Community Awards recipients https://youtu.be/noHn5fEbBwA?t=2708 ."
2 | name: "Keynote (day2 13:00~), Lori Ann Shepherd: \"What is Bioconductor? : How the Core Team Plays an Essential Role\""
3 | position: "Roswell Park Comprehensive Cancer Center, USA"
4 | avatar: "img/speakers/Lori.png"
5 |
--------------------------------------------------------------------------------
/data/speakers/7.yaml:
--------------------------------------------------------------------------------
1 | text: "Soroor Hediyeh-zadeh is a graduate research student in the department of medical biology (Walter and Eliza Hall Institute) at The University of Melbourne. Previously, She was a Research Assistant (RA) in A/Prof. Melissa Davis's Lab at the Bioinformatics Division in WEHI, and a Masters student at The University of Melbourne in the School of Mathematics and Statistics. She is broadly interested in developing and studying machine learning and statistical models for the analysis of transcriptomics and proteomics data."
2 | name: "Invited talk (day2 14:30~), Soroor Hediyeh-zadeh: \"MsImpute: Estimation of missing peptide intensity values in label-free mass spectrometry\""
3 | position: "Walter and Eliza Hall Institute of Medical Research, Australia"
4 | avatar: "img/speakers/Soroorh.png"
5 |
--------------------------------------------------------------------------------
/data/speakers/3.yaml:
--------------------------------------------------------------------------------
1 | text: "Stefano Mangiola is a postdoctoral fellow at Walter and Eliza Hall Institute of Medical Research, focused on tumor microenvironment. Maria Doyle is an application and training specialist for research computing at Peter MacCallum Cancer Centre. Stefano and Maria have developed a suite of software that integrates the tidyverse framework and transcriptomics analysis, and publishes them as Bioconductor packages. As part of this effort, Stefano and Maria developed an interface for Seurat with tidyverse, which is published in https://doi.org/10.1093/bioinformatics/btab404 ."
2 | name: "Invited talk (day1 14:30~), Stefano Mangiola: \"Interfacing Seurat with the R tidy universe\""
3 | position: "Walter and Eliza Hall Institute of Medical Research, Australia"
4 | avatar: "img/speakers/StefanoAndMaria.png"
5 |
--------------------------------------------------------------------------------
/data/speakers/93.yaml:
--------------------------------------------------------------------------------
1 | text: "Takeya Kasukawa is the team leader of RIKEN Center for Integrative Medical Sciences, Laboratory for Large-Scale Biomedical Data Technology. His major is the development of data management technology that will lead to new discoveries in the field of biomedical science. He has maintained the database of the international collaborative research \"FANTOM (Functional ANnoTation of Mammalian Genome) Project\". This database is widely provided to the research community and is expected to contribute to the elucidation of biological phenomena."
2 | name: "Keynote (day4 13:00~), Takeya Kasukawa: \"FANTOM project and data resource for understanding the transcription in the mammalian genomes\""
3 | position: "RIKEN Center for Integrative Medical Sciences, Japan"
4 | avatar: "img/speakers/TakeyaKasukawa.jfif"
5 |
6 |
--------------------------------------------------------------------------------
/themes/hugo-universal-theme/layouts/partials/map.html:
--------------------------------------------------------------------------------
1 | {{ if .Site.Params.enableGoogleMaps }}
2 | {{ if isset .Site.Params "latitude" }}
3 | {{ if isset .Site.Params "longitude" }}
4 |
22 | {{ end }}
23 | {{ end }}
24 | {{ end }}
25 |
--------------------------------------------------------------------------------
/data/speakers/1.yaml:
--------------------------------------------------------------------------------
1 | text: "Hiroshi Tsugawa got his PhD from Osaka University in 2012, Japan. His major is systems biology through computational mass spectrometry (CompMS) to deepen the understanding of metabolisms in living organisms. Employing CompMS, he could develop a data processing pipeline for complex MS data and identify unknown metabolites using computational analysis of mass fragmentation. The awards he received are RIKEN BAIHO Award (2020), Top 40 Under 40 of “The Analytical Science” (2018), and RIKEN Incentive Research Award (2016). Since 2021, he is working as an associate professor at the Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology."
2 | name: "Keynote (day1 13:10~), Hiroshi Tsugawa: \"Decoding mass spectrometry data to understand the metabolisms of living organisms\""
3 | position: "Tokyo University of Agriculture and Technology, Japan"
4 | avatar: "img/speakers/HiroshiTsugawa.gif"
5 |
--------------------------------------------------------------------------------
/themes/hugo-universal-theme/layouts/partials/widgets/categories.html:
--------------------------------------------------------------------------------
1 | {{ if .Site.Params.widgets.categories }}
2 | {{ if isset .Site.Taxonomies "categories" }}
3 | {{ if not (eq (len .Site.Taxonomies.categories) 0) }}
4 |
37 |
38 |
39 |
--------------------------------------------------------------------------------
/LICENSE:
--------------------------------------------------------------------------------
1 | MIT License
2 |
3 | Copyright (c) 2020 Mikhail Dozmorov
4 |
5 | Permission is hereby granted, free of charge, to any person obtaining a copy
6 | of this software and associated documentation files (the "Software"), to deal
7 | in the Software without restriction, including without limitation the rights
8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 |
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 |
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 |
--------------------------------------------------------------------------------
/themes/hugo-universal-theme/LICENSE:
--------------------------------------------------------------------------------
1 | The MIT License (MIT)
2 |
3 | Copyright (c) 2016 DevCows
4 |
5 | Permission is hereby granted, free of charge, to any person obtaining a copy
6 | of this software and associated documentation files (the "Software"), to deal
7 | in the Software without restriction, including without limitation the rights
8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 |
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 |
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 |
--------------------------------------------------------------------------------
/docs/sitemap.xml:
--------------------------------------------------------------------------------
1 |
2 |
4 |
5 | /
6 | 2020-10-16T18:52:14-04:00
7 |
8 | /posts/my-first-post/
9 | 2020-10-16T18:52:14-04:00
10 |
11 | /posts/
12 | 2020-10-16T18:52:14-04:00
13 |
14 | /categories/
15 |
16 | /code/
17 |
18 | /contact/
19 |
20 | /contributions/
21 |
22 | /jobs/
23 |
24 | /organizers/
25 |
26 | /conferences/
27 |
28 | /registration/
29 |
30 | /schedule/
31 |
32 | /schedule_iframe/
33 |
34 | /submissions/
35 |
36 | /tags/
37 |
38 | /workshops/
39 |
40 | /code-mandarin/
41 |
42 | /code-japanese/
43 |
44 |
45 |
--------------------------------------------------------------------------------
/themes/hugo-universal-theme/layouts/partials/see_more.html:
--------------------------------------------------------------------------------
1 | {{ if isset .Site.Params "see_more" }}
2 | {{ if .Site.Params.see_more.enable }}
3 |
4 |
5 |
108 |
109 |
110 | {{ partial "scripts.html" . }}
111 |
112 |
113 |
114 |
--------------------------------------------------------------------------------
/content/code.md:
--------------------------------------------------------------------------------
1 | +++
2 | title = "Code of conduct"
3 | description = "Code of conduct"
4 | +++
5 |
6 | This code of conduct is developed for the virtual Bioc Asia 2021 conference. For more details, see the [Bioconductor Code of Conduct](https://www.bioconductor.org/about/code-of-conduct/)
7 |
8 |
9 | ## Social media policy
10 |
11 | Images and content from talks, workshops, and posters may be shared publicly through social media (Twitter, etc.). Videos will be released on the [Youtube Bioconductor channel](https://www.youtube.com/user/bioconductor). Please, inform the organizing committee as soon as possible if you don't wish your presentation material to be shared.
12 |
13 | ## The _Bioconductor_ conference aims to provide a supportive, collegial, and harassment-free environment
14 |
15 | _Bioconductor_ is dedicated to providing a supportive, collegial, and harassment-free
16 | conference experience for everyone, regardless of:
17 | * gender, gender identity and expression, sexual orientation, disability,
18 | physical appearance, body size, race, age, or religion.
19 | * intellectual position: approaches to data analysis, software preferences, coding style, scientific perspective, etc.
20 |
21 | The Virtual Event Code of Conduct applies to BiocAsia2021 virtual events and communications, including but not limited to the virtual platform, talks, workshops, poster sessions, social activities, slack, online and social media communications. We do not tolerate harassment, intimidation, or bullying of conference participants. Sexual language and imagery are not appropriate in presentations, communications, in online venues, including chats.
22 |
23 | Conference participants violating these rules may be sanctioned or expelled from the conference,
24 | at the discretion of the conference organizers. Our anti-harassment policy can be found at [https://bioc2020.bioconductor.org/code_of_conduct](https://bioc2020.bioconductor.org/code_of_conduct)
25 |
26 | ## Examples of unacceptable harassment, intimidation, and bullying behavior
27 |
28 | Harassment includes, but is not limited to:
29 |
30 | * Making comments in chats, to an audience or personally, that belittle or demean another person
31 | * Sharing sexual images online
32 | * Harassing photography or recording
33 | * Sustained disruption of talks or other events
34 | * Unwelcome sexual attention
35 | * Advocating for, or encouraging, any of the above behavior
36 |
37 | Intimidation and bullying include, but are not limited to:
38 |
39 | * Aggressive or browbeating behavior directed at someone during a public presentation
40 | * Mocking or insulting another person's intellect, work, perspective, or question/comment
41 | * Making reference to someone's gender, gender identity and expression, sexual orientation, disability,
42 | physical appearance, body size, race, age, religion, or other personal attributes in the context of a scientific
43 | discussion
44 | * Deliberately making someone feel unwelcome
45 |
46 | ### Enforcement
47 |
48 | Participants asked to stop any harassing behavior are expected to comply immediately.
49 |
50 | If a participant engages in harassing behavior, event organizers retain the right to take any actions to keep the event a welcoming environment for all participants. This includes warning the offender or expulsion from the conference.
51 |
52 | Event organizers may take action to redress anything designed to, or with the clear impact of, disrupting the event or making the environment hostile for any participants.
53 |
54 | We expect participants to follow these rules at all event venues and event-related online activities.
55 |
56 | ### Reporting
57 |
58 | If someone makes you or anyone else feel unsafe or unwelcome, please report it as soon as possible.
59 | Harassment and other code of conduct violations reduce the value of our event for everyone.
60 | We want you to be happy at our event. People like you make our event a better place.
61 |
62 | You can make a report either personally or anonymously.
63 |
64 | #### Anonymous or Non-anonymous Report
65 |
66 | You can make an anonymous or non-anonymous report here: [https://tinyurl.com/bioccomplaint](https://tinyurl.com/bioccomplaint). It is a free-form text box that will be forwarded to conference organizers.
67 |
68 | We can't follow up an anonymous report with you directly, but we will fully investigate it and take whatever action is necessary to prevent a recurrence.
69 |
70 | #### Personal Report
71 |
72 | You can make a personal report with any of the conference anti-harassment committee: Kozo Nishida.
73 |
74 | When taking a personal report, our staff will ensure you are safe and cannot be overheard. They may involve other event staff to ensure your report is managed properly. Once safe, we'll ask you to tell us about what happened. This can be upsetting, but we'll handle it as respectfully as possible, and you can bring someone to support you. You won't be asked to confront anyone, and we won't tell anyone who you are.
75 |
76 | ### Code of Conduct violation reports
77 |
78 | * Email: [code-of-conduct@bioconductor.org](mailto:workshop@bioconductor.org?subject=BioC2019%20code-of-conduct)
79 | * Anonymous Code of Conduct violation reports: [https://tinyurl.com/bioccomplaint](https://tinyurl.com/bioccomplaint)
80 |
--------------------------------------------------------------------------------
/docs/img/clients/logo.svg:
--------------------------------------------------------------------------------
1 |
2 |
134 |
--------------------------------------------------------------------------------
/static/img/clients/logo.svg:
--------------------------------------------------------------------------------
1 |
2 |
134 |
--------------------------------------------------------------------------------
/themes/hugo-universal-theme/layouts/partials/head.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 | {{ $title_plain := .Title | markdownify | plainify }}
7 | {{ $title_plain }}
8 |
9 | {{ $keywords := .Site.Params.defaultKeywords | default (slice "" | first 0) }}
10 | {{ if isset .Params "tags" }}{{ range .Params.tags }}{{ $keywords = $keywords | append . }}{{ end }}{{ end }}
11 | {{ if isset .Params "keywords" }}{{ range .Params.keywords }}{{ $keywords = $keywords | append . }}{{ end }}{{ end }}
12 | {{ if gt (len $keywords) 0 }}
13 |
14 | {{ end }}
15 | {{ $description_plain := default .Site.Params.defaultDescription .Description | markdownify | plainify }}
16 |
17 |
18 | {{ hugo.Generator }}
19 |
20 |
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 | {{ with .Site.Params.style }}
32 |
33 | {{ else }}
34 |
35 | {{ end }}
36 |
37 |
38 |
39 |
40 |
41 | {{ `
42 |
46 | ` | safeHTML }}
47 |
48 |
49 |
50 |
51 |
52 |
53 |
54 |
55 |
56 |
57 |
58 |
59 |
60 | {{ $is_blog := and (eq .Type "blog") (eq .Kind "page") }}
61 | {{ $has_image := isset .Params "banner" }}
62 | {{ $image := cond $has_image .Params.banner (.Site.Params.default_sharing_image | default "img/sharing-default.png") }}
63 | {{ $is_valid_image := print "static/" $image | fileExists }}
64 | {{ if $is_valid_image }}
65 | {{ $image_ext := path.Ext $image }}
66 |
67 |
68 |
69 |
70 |
71 |
72 |
73 |
74 | {{ with .Params.banner_alt }}{{ end }}
75 | {{ $image_local := printf "/static/%s" $image}}
76 | {{ with (imageConfig $image_local) }}
77 |
78 |
79 | {{ end }}
80 | {{ end }}
81 | {{ with .Lastmod }}{{ end }}
82 | {{ if $is_blog }}
83 | {{ with .Param "facebook_site" }}{{ end }}
84 | {{ with .Param "facebook_author" }}{{ end }}
85 | {{ with .Params.categories }}{{ end }}
86 | {{ range .Params.tags }}
87 | {{ end }}
88 | {{ if gt .ExpiryDate .PublishDate }}{{ end }}
89 | {{ with .PublishDate }}{{ end }}
90 | {{ with .Lastmod }}{{ end }}
91 | {{ end }}
92 |
93 |
94 |
95 | {{ with .Param "twitter_site" }}{{ end }}
96 |
97 | {{ if $is_valid_image }}
98 |
99 | {{ end }}
100 |
101 | {{ with .Param "twitter_author" }}{{ end }}
102 |
103 |
104 |
--------------------------------------------------------------------------------
/config.toml:
--------------------------------------------------------------------------------
1 | # baseurl = "https://bioconductor.github.io/BiocAsia2021/"
2 | baseurl = "/"
3 | title = "BioC Asia 2021"
4 | theme = "hugo-universal-theme"
5 | # themesDir = "../.."
6 | publishDir = "docs"
7 | #canonifyurls = true
8 | languageCode = "en-us"
9 | # Site language. Available translations in the theme's `/i18n` directory.
10 | defaultContentLanguage = "en"
11 | # Enable comments by entering your Disqus shortname
12 | # disqusShortname = "devcows"
13 | # Enable Google Analytics by entering your tracking code
14 | # googleAnalytics = ""
15 |
16 | # Define the number of posts per page
17 | paginate = 10
18 |
19 | [menu]
20 |
21 | # Main menu
22 |
23 | [[menu.main]]
24 | identifier="home"
25 | name = "Home"
26 | url = "/"
27 | weight = 1
28 |
29 | [[menu.main]]
30 | identifier="schedule"
31 | name = "Schedule"
32 | url = "/schedule/"
33 | weight = 2
34 |
35 | #[[menu.main]]
36 | # identifier = "registration"
37 | # name = "Registration"
38 | # url = "/registration/"
39 | # weight = 3
40 |
41 | [[menu.main]]
42 | identifier = "contributions"
43 | name = "Contributed talks"
44 | url = "/contributions/"
45 | weight = 3
46 |
47 | [[menu.main]]
48 | identifier="workshops"
49 | name = "Workshops"
50 | url = "/workshops/"
51 | weight = 4
52 |
53 | #[[menu.main]]
54 | # identifier="submissions"
55 | # name = "Submissions"
56 | # url = "/submissions/"
57 | # weight = 6
58 |
59 | [[menu.main]]
60 | identifier = "code"
61 | name = "Code of conduct"
62 | url = "/code/"
63 | weight = 5
64 |
65 | [[menu.main]]
66 | identifier = "code-Mandarin"
67 | name = "行为准则"
68 | url = "/code-Mandarin/"
69 | weight = 6
70 |
71 | [[menu.main]]
72 | identifier = "code-Japanese"
73 | name = "行動規範"
74 | url = "/code-Japanese/"
75 | weight = 7
76 |
77 | [[menu.main]]
78 | identifier = "jobs"
79 | name = "求人"
80 | url = "/jobs/"
81 | weight = 8
82 |
83 | [[menu.main]]
84 | identifier = "conferences"
85 | name = "Past conferences"
86 | url = "/conferences/"
87 | weight = 9
88 |
89 | [[menu.main]]
90 | identifier = "organizers"
91 | name = "Organizers"
92 | url = "/organizers/"
93 | weight = 10
94 |
95 | # [[menu.main]]
96 | # identifier = "contact"
97 | # name = "Contact"
98 | # url = "/contact/"
99 | # weight = 8
100 |
101 | # Top bar social links menu
102 |
103 | [[menu.topbar]]
104 | weight = 1
105 | name = "GitHub"
106 | url = "https://github.com/Bioconductor"
107 | pre = ""
108 |
109 | # [[menu.topbar]]
110 | # weight = 2
111 | # name = "Facebook"
112 | # url = "http://facebook.com"
113 | # pre = ""
114 |
115 | [[menu.topbar]]
116 | weight = 3
117 | name = "Twitter"
118 | url = "https://twitter.com/Bioconductor"
119 | pre = ""
120 |
121 | # [[menu.topbar]]
122 | # weight = 4
123 | # name = "Email"
124 | # url = "mailto:kozo.nishida@gmail.com"
125 | # pre = ""
126 |
127 | [[menu.topbar]]
128 | weight = 5
129 | name = "Slack"
130 | url = "http://biocasia2021.slack.com/"
131 | pre = ""
132 |
133 | [params]
134 | viewMorePostLink = "/blog/"
135 | author = "DevCows"
136 | defaultKeywords = ["devows", "hugo", "go"]
137 | mainSections = ["blog"]
138 | defaultDescription = "Site template made by devcows using hugo"
139 |
140 | # Social media
141 | facebook_site = "" # the Facebook handle of your site ('https://www.facebook.com/HANDLE')
142 | twitter_site = "Bioconductor" # the Twitter handle of your site (without the '@')
143 | default_sharing_image = "img/sharing-default.png"
144 |
145 | # Google Maps widget: If `googleMapsApiKey` is not set, no key will be passed to Google (which likely results in a broken map widget).
146 | enableGoogleMaps = false
147 | googleMapsApiKey = "AIzaSyCFhtWLJcE30xOAjcbSFi-0fnoVmQZPb1Y"
148 |
149 | latitude = "-12.043333"
150 | longitude = "-77.028333"
151 |
152 | # Style options: default (light-blue), blue, green, marsala, pink, red, turquoise, violet
153 | style = "red"
154 |
155 | # Since this template is static, the contact form uses www.formspree.io as a
156 | # proxy. The form makes a POST request to their servers to send the actual
157 | # email. Visitors can send up to a 1000 emails each month for free.
158 | #
159 | # What you need to do for the setup?
160 | #
161 | # - set your email address under 'email' below
162 | # - upload the generated site to your server
163 | # - send a dummy email yourself to confirm your account
164 | # - click the confirm link in the email from www.formspree.io
165 | # - you're done. Happy mailing!
166 | #
167 | # Enable the contact form by entering your Formspree.io email
168 | email = "knishida@riken.jp"
169 | contact_form_ajax = false
170 |
171 | about_us = "
Bioconductor conference highlights current developments within and beyond the Bioconductor project.
183 | """
184 |
185 | [Permalinks]
186 | blog = "/blog/:year/:month/:day/:filename/"
187 |
188 | # Enable or disable top bar with social icons
189 | [params.topbar]
190 | enable = true
191 | text = """
Join/follow our community
192 |
193 |
194 |
195 | """
196 |
197 | # Enable and disable widgets for the right sidebar
198 | [params.widgets]
199 | categories = true
200 | tags = true
201 | search = true
202 |
203 | [params.carousel]
204 | enable = true
205 | # All carousel items are defined in their own files. You can find example items
206 | # at 'exampleSite/data/carousel'.
207 | # For more informtion take a look at the README.
208 |
209 | [params.features]
210 | enable = false
211 | # All features are defined in their own files. You can find example items
212 | # at 'exampleSite/data/features'.
213 | # For more informtion take a look at the README.
214 |
215 | [params.testimonials]
216 | enable = false
217 | # All testimonials are defined in their own files. You can find example items
218 | # at 'exampleSite/data/testimonials'.
219 | # For more informtion take a look at the README.
220 | title = "Testimonials"
221 | subtitle = "We have worked with many clients and we always like to hear they come out from the cooperation happy and satisfied. Have a look what our clients said about us."
222 |
223 | [params.speakers]
224 | enable = true
225 | # All testimonials are defined in their own files. You can find example items
226 | # at 'exampleSite/data/speakers'.
227 | # For more informtion take a look at the README.
228 | title = "Speakers (The following times are Japan time [UTC+09:00])"
229 | # subtitle = "Confirmed speakers"
230 |
231 | [params.see_more]
232 | enable = false
233 | icon = "far fa-file-alt"
234 | title = "Do you want to see more?"
235 | subtitle = "We have prepared for you more than 40 different HTML pages, including 5 variations of homepage."
236 | link_url = "#"
237 | link_text = "Check other homepages"
238 |
239 | [params.clients]
240 | enable = true
241 | # All clients are defined in their own files. You can find example items
242 | # at 'exampleSite/data/clients'.
243 | # For more informtion take a look at the README.
244 | title = "Our Supporters"
245 | subtitle = ""
246 |
247 | [params.recent_posts]
248 | enable = false
249 | title = "From our blog"
250 | subtitle = "Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo."
251 |
252 |
--------------------------------------------------------------------------------
/content/contributions.md:
--------------------------------------------------------------------------------
1 | +++
2 | title = "Contributed talks"
3 | description = "Contributed talks"
4 | +++
5 |
6 | **THE FOLLOWING TIMES ARE ALL JAPAN TIME (UTC+09:00)**
7 |
8 | ## Day1
9 |
10 | ### (15:00~) Omar El-Ashkar: "rGenomeTracks: Extending epigenetic visualization methods in R"
11 |
12 | High throughput sequencing technologies have been proved useful in a plethora of omics. Epigenomics is an area of active research that innovatively blends different biological techniques with sequencing to gain new insight into epigenetic regulations like chromatin accessibility, genome topology and nucleosome positioning. One of the cornerstones of analyzing such data is to be able to visualize it. R has been limited by the difficulty of visualizing epigenetic data in a quick way ought to data size. Hence we created rGenomeTracks, an R package based on pyGenomeTracks python package that offers customizable, publication-ready figures in a quick way. rGenomeTracks make it easier for R users to have a smooth workflow without the need of interacting with python.
13 |
14 | - https://github.com/OAshkar/rGenomeTracks
15 |
16 | ### (15:30~) Xinyi Lin: "Differential composition analysis of single-cell data"
17 |
18 | Single cell profiling technology such as single-cell RNA-seq (scRNA-seq) enables high throughput discovery and characterisation of diverse cell types or cell states in a population of cells. This ability has given rise to new statistical problems in robust quantification and comparison of cell-type proportion.. It remains challenging to effectively detect differential compositions of cell types when comparing samples coming from different conditions or along with continuous covariates, partly due to the small number of replicates and high uncertainty of cell clustering. Here, we introduce a new statistical model, DCATS, for differential composition analysis in single cells in a framework of beta-binomial regression. It leverages a confusion matrix to correct the bias of clustering and allows pre-estimated parameters across all cell types to account for its uncertainty. It also allows us to regress out the influence of confounding covariates except for the condition factor. Through multiple simulated and experimental data sets, we demonstrate the high effectiveness of DCATS in identifying variable cell types in various experiment designs. Combining the differential genes analysis, cell-cell interaction analysis, and other scRNA-seq analysis, DCATS deepens our understanding of cell types differential composition and gain biological insight.
19 |
20 | - https://github.com/huangyh09/DCATS/
21 |
22 | ## Day2
23 |
24 | ### (15:00~) Mahmoud Ahmed: "LINPS: a database for cancer-cell-specific perturbations of biological networks"
25 |
26 | Screening for potential cancer therapies using existing large datasets of drug perturbations requires expertise and resources not available to all.
27 | This is often a barrier for lab scientists to tap into these valuable resources.
28 | To address these issues, one can take advantage of prior knowledge especially those coded in standard formats such as causal biological networks (CBN).
29 | Large datasets can be converted into appropriate structures, analyzed once and the results made freely available in easy-to-use formats.
30 | We used the Library of Integrated Cellular Signatures to model the cell-specific effect of hundreds of drug treatments on gene expression.
31 | These signatures were then used to predict the effect of the treatments on several CBN using the network perturbation amplitudes analysis.
32 | We packaged the pre-computed scores in a database with an interactive web interface.
33 | The intuitive user-friendly interface can be used to query the database for drug perturbations and quantify their effect on multiple key biological functions in cancer cell lines.
34 | In addition to describing the process of building the database and the interface, we provide a realistic use case to explain how to use and interpret the results.
35 | To sum, we pre-computed cancer-cell-specific perturbation amplitudes of several biological networks and made the output available in a database with an interactive web interface.
36 |
37 | - https://doi.org/10.1093/database/baab048
38 |
39 | ### (15:30~) Pengyi Yang: "PhosR enables processing and functional analysis of phosphoproteomic data"
40 |
41 | Mass spectrometry (MS)-based phosphoproteomics has revolutionized our ability to profile phosphorylation-based signaling in cells and tissues on a global scale.
42 | In this talk, I will introduce PhosR, a set of tools and methodologies implemented in a Bioconductor R package to allow the comprehensive analysis of phosphoproteomic data.
43 | PhosR enables processing steps such as imputation, normalization, and functional analysis such as kinase activity inference and signalome construction.
44 | Together, PhosR facilitates interpretation and discovery from large-scale phosphoproteomic data sets.
45 |
46 | - https://bioconductor.org/packages/release/bioc/html/PhosR.html
47 | - https://github.com/PYangLab/PhosR
48 | - https://pyanglab.github.io/PhosR/
49 |
50 | ## Day3
51 |
52 | ### (15:00~) Luke C. Gandolfo: "Untangling batch and biological effects with RLE plots"
53 |
54 | Data visualisation is an essential part of analysing high-dimensional gene expression data, e.g. RNA-seq. One reason for such visualisation is to detect the presence of technical variation, e.g. batch effects, and to check the success of our attempts to remove such variation via normalisation.
55 | However, in situations where the biological conditions of interest are significantly confounded with the factors producing technical variation, common visualisation approaches, e.g. PCA plots, can be poor tools, since such plots are sensitive to both technical and biological effects.
56 | Relative log expression (RLE) plots, on the other hand, are sensitive to technical effects but insensitive, i.e. highly robust, to biological effects, making them an ideal tool for visualising the presence of technical variation in situations involving confounding.
57 | RLE plots also have significant advantages over similar robust plots, e.g. boxplots.
58 | These claims are demonstrated through the use of real data examples and statistical simulation.
59 |
60 | - https://doi.org/10.1371/journal.pone.0191629
61 |
62 | ### (15:30~) Kozo Nishida: "[BoF] Improving accessibility to Bioconductor in Japan"
63 |
64 | Accessibility to Bioconductor's information resources varies greatly between English and other languages. Bioconductor users in Japan are not small, but the number of developers is significantly smaller than in Europe and the United States.
65 | This BOF introduces attempts to improve accessibility to Bioconductor in Japan, along with the activities of BioPackathon, the Software Carpentry Japanese Team, and the Bioconductor Community Advisory Board.
66 | BioPacakthon is a community that promotes bio software packaging and provides Bioconductor packaging information in Japanese. BioPackathon also organizes BioC Asia 2021 and has conducted survey to overcome language barriers.
67 | The Software Carpentry Japanese Team is a community that localizes Carpentries teaching materials in Japanese.
68 | Bioconductor is creating Carpentries-style teaching materials, and it is important for Bioconductor that Carpentries' activities become active in Japan.
69 | The Bioconductor Community Advisory Board has a board member in Japan, and is planning to improve accessibility from Japan to Bioconductor in line with the CZI EOSS project.
70 | In this BOF, the above will be explained in slides and the future prospects will be introduced.
71 |
72 | ## Day4
73 |
74 | ### (15:00~) Yohei Kumagai (熊谷洋平): "[Supporter talk (後援トーク)] Introduction of academic recruiting platform tayo (アカデミック求人プラットフォーム tayo の紹介)"
75 | **This talk will be conducted in Japanese.**
76 | **本トークは日本語で行われます。**
77 |
78 | Compared to employment in the private sector, there is a lack of information about entering graduate school, and this has become a bottleneck in the flow of human resources in academia.
79 | This presentation will introduce [tayo](https://tayo.jp/)’s efforts to revitalize the flow of human resources in academia and create a world where a diverse people can aim to become scientists.
80 |
81 | 民間に比べて大学院への進学に関する情報が不足しており、これが学界の人材の流れのボトルネックになっています。
82 | このプレゼンテーションでは、学界における人材の流れを活性化し、多様な人々が科学者になることを目指すことができる世界を創造するための [tayo](https://tayo.jp/) の取り組みを紹介します。
83 |
84 | ### (15:30~) Zuguang Gu: "spiralize: an R Package for Visualizing Data on Spirals"
85 |
86 | The spiral layout has two major advantages for data visualization. First, it is able to visualize data with long axes, which greatly improves the resolution of visualization. Second, it is efficient for time series data to reveal periodic patterns. Here we present the R package spiralize that provides a general solution for visualizing data on spirals. spiralize implements numerous graphics functions so that self-defined high-level graphics can be easily implemented by users. The spiralize package is available at https://CRAN.R-project.org/package=spiralize.
87 |
--------------------------------------------------------------------------------
/docs/404.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 | 404 Page not found
11 |
12 |
13 |
14 |
15 |
16 |
17 |
18 |
19 |
20 |
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
37 |
38 |
39 |
40 |
41 |
42 |
43 |
47 |
48 |
49 |
50 |
51 |
52 |
53 |
54 |
55 |
56 |
57 |
58 |
59 |
60 |
61 |
62 |
63 |
64 |
65 |
66 |
67 |
68 |
69 |
70 |
71 |
72 |
73 |
74 |
75 |
76 |
77 |
78 |
79 |
80 |
81 |
82 |
90 |