11 |
11 |
12 | 
| Martin Morgan | Roswell Park Comprehensive Cancer Center |
12 | | 
| Xuegong Zhang | Tsinghua University |
13 | | 
| Matthew Ritchie | Walter and Eliza Hall Institute of Medical Research |
14 | | 
| Julie Zhu | University of Massachusetts, Medical School |
15 | | 
| Peter Hickey | Walter and Eliza Hall Institute of Medical Research |
16 | | 
| Jin Gu | Tsinghua University |
17 | | 
| Rui Jiang | Tsinghua University |
18 | | 
| Qian Liu | Roswell Park Comprehensive Cancer Center |
19 |
20 |
21 |
--------------------------------------------------------------------------------
/docs/call-for-abstracts.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: default
3 | ---
4 |
5 | {% include header.md %}
6 |
7 | ## Call for abstracts
8 |
9 | The conference will feature a poster session and a number of selected short talks (15mins), lightning talks (5mins) and workshops (55 mins). To be considered for such a presentation, please fill out the [application form](https://mccb.umassmed.edu/BiocAsia2020/) by 25th September 2020.
10 |
11 | ## F1000Research
12 |
13 | We are delighted to announce that all posters and slides from the conference this year will be hosted on the F1000Research [Bioconductor Gateway](https://f1000research.com/gateways/bioconductor/about-this-gateway) with the "BiocAsia2020" area. The submission is free of charge, and published posters on F1000Research will receive a digital object identifier (DOI). This is a great opportunity to get credit for your work and increase its visibility and impact. We also encourage conference attendees to contribute articles on Bioconductor workflows or packages to the Bioconductor gateway on F1000Research (Article Processing Charges apply).
14 |
15 | ### Poster/talk slides submission to F1000Research
16 |
17 | The BiocAsia2020 poster submission on F1000Research is still open. All are encouraged to submit their posters to the [Bioconductor BioC Asia 2020 conference gateway](https://f1000research.com/gateways/bioconductor/biocasia2020) before Oct. 10th (CST). There are no formatting requirements for posters (feel free to be creative); however, for those who would like to use it, a [poster template](https://drive.google.com/file/d/1N3pDnixeVwRFrjQrSJL9eziXq4RpcfaT/view) is available. Inclusion of the Bioconductor logo and/or #BioCAsia2020 is encouraged. For more submission details, please refer to the [Poster & Slides Guidelines](https://f1000research.com/gateways/bioconductor/for-authors/posters-and-slides-guidelines).
18 |
19 |
20 |
21 |
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/docs/past_conferences.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: default
3 | ---
4 |
5 | {% include header.md %}
6 |
7 | ## Bioconductor Asia conferences and course materials
8 | - [Bioconductor Asia 2019](https://bioconductor.github.io/BiocAsia/), Sydney, Australia
9 | - [Bioconductor Asia 2018](https://docs.google.com/document/d/1MT3-4fhHmwxqf72Mj5FIsaOwEYKsHlij114j1-muMu0/edit?usp=sharing), Melbourne, Australia
10 | - [Bioconductor Asia 2017](https://docs.google.com/document/d/1XH1CUFMyuyJk0MVaEj-6nLLHcvZuV4WR7vt-LteomMs/edit?usp=sharing), Adelaide, Australia
11 | - [Bioconductor Asia 2016](https://docs.google.com/document/d/1IswBic7dQ4dJpEawYHfIjC6D-fXuoMtc-iKbM7juN2E/edit?usp=sharing), Brisbane, Australia
12 | - [Bioconductor Asia 2015](https://docs.google.com/document/d/1DrUYi96ZnIeOgjOHiWzoNRNrwOxwGwfMp1qkOwVKBrA/edit?usp=sharing), Tokyo, Japan
13 |
14 | ## Bioconductor main conferences and course materials
15 |
16 | - [Bioconductor 2020](https://bioc2020.bioconductor.org/), Boston, USA
17 | - [Bioconductor 2019](https://bioc2019.bioconductor.org/), New York, USA
18 | - [Bioconductor 2018](https://bioc2018.bioconductor.org/), Toronto, Canada
19 | - [Bioconductor 2017](https://bioconductor.org/help/course-materials/2017/BioC2017/), Boston, USA
20 | - [Bioconductor 2016](https://bioconductor.org/help/course-materials/2016/BioC2016/), Stanford, USA
21 | - [Bioconductor 2015](https://bioconductor.org/help/course-materials/2015/BioC2015/), Seattle, USA
22 | - [Bioconductor 2014](https://bioconductor.org/help/course-materials/2014/BioC2014/), Boston, USA
23 | - [Bioconductor 2013](https://bioconductor.org/help/course-materials/2013/BioC2013/), Seattle, USA
24 | - [Bioconductor 2012](https://bioconductor.org/help/course-materials/2012/BioC2012/), Seattle, USA
25 | - [Bioconductor 2011](https://bioconductor.org/help/course-materials/2011/BioC2011/), Seattle, USA
26 | - [Bioconductor 2010](https://bioconductor.org/help/course-materials/2010/BioC2010/), Seattle, USA
27 | - [Bioconductor 2009](https://bioconductor.org/help/course-materials/2009/BioC2009/), Seattle, USA
28 | - [Bioconductor 2008](https://bioconductor.org/help/course-materials/2008/BioC2008/), Seattle, USA
29 | - [Bioconductor 2007](https://bioconductor.org/help/course-materials/2007/BioC2007/), Seattle, USA
30 | - [Bioconductor 2006](https://bioconductor.org/help/course-materials/2006/BioC2006/), Seattle, USA
31 | - [Bioconductor 2005](https://bioconductor.org/help/course-materials/2005/BioC2005/), Seattle, USA
32 |
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/docs/schedule.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: default
3 | ---
4 |
5 | {% include header.md %}
6 |
7 | # Calendar agenda
8 |
9 | Schedule is based on Beijing Time / China Standard Time (UTC + 8),
10 | Please change to your preferred "Time zone" in this interactive
11 | calendar. All sessions include Q&A time.
12 |
13 |
14 |
15 | # Agenda
16 |
17 | | Time | Track | Speaker |
18 | |--------------------------|----------------------|---------------------------------------------------------|
19 | | **Thursday, 2020-10-15** | | |
20 | | 7:45-7:50 AM | BiocAsia2020 Opening | Dr. Jin Gu |
21 | | 7:50-8:00 AM | Opening Remark | Dr. Martin Morgan |
22 | | 8:00-8:55 AM | Keynote Talk | Dr. Robert Gentleman |
23 | | 9:00-9:55 AM | Invited Talks | Drs. Lihua Julie Zhu, Qiangfeng Zhang |
24 | | 10:00-10:15 AM | Break | |
25 | | 10:15-10:45 AM | Contributed Talks | Drs. Drs. Pol Castellano-Escuder, Mahmoud Ahmed |
26 | | 10:50-11:45 AM | workshops (parallel) | Drs. Xueyi Dong (track 1), Dr. Jianhong Ou (track 2) |
27 | | | | |
28 | | **Friday, 2020-10-16** | | |
29 | | 8:00-8:55 AM | Invited Talks | Drs. Saskia Freytag, Kai Ye |
30 | | 9:00-9:55 AM | Invited Talks | Drs. Charity Law, Koki Tsuyuzaki |
31 | | 10:00-10:15 AM | Break | |
32 | | 10:15-10:45 AM | Contributed Talks | Drs. Christina Azodi, Paul Harrison |
33 | | 10:50-11:45 AM | workshops (parallel) | Drs. Saskia Freytag (track 1), Qian Liu (track 2) |
34 | | | | |
35 | | **Saturday, 2020-10-17** | | |
36 | | 9:00-9:55 AM | Keynote Talk | Dr. Yi Xing |
37 | | 10:00-10:55 AM | Invited Talks | Drs. Lin Hou, Guangchuang Yu |
38 | | 11:00-11:15 AM | Break | |
39 | | 11:15-11:45 AM | Contributed Talks | Drs. Joseph Lee, Ms. Yue You |
40 | | 11:50 AM-12:45 PM | workshops (parallel) | Drs. Shuangbin Xu (track 1), Stefano Mangiola (track 2) |
41 | | | | |
42 | | **Sunday, 2020-10-18** | | |
43 | | 9:00-9:55 AM | Keynote Talk | Dr. Xuegong Zhang |
44 | | 10:00-10:23 AM | Invited Talks | Dr. Tingting Li |
45 | | 10:25-10:40 AM | Contributed talks | Dr. Xueyi Dong |
46 | | 10:40-10:45 AM | Lightning talks | Shixiang Wang |
47 | | 10:45-11:00 AM | Poster session | |
48 | | 11:00-11:15 AM | Break | |
49 | | 11:15-11:45 AM | Contributed Talks | Mr. Shian Su, Dr Antonio Colaprico |
50 | | 11:50-12:45 PM | Workshops (parallel) | Drs. Luyi Tian (track 1), Hani Jieun Kim (track 2) |
51 | | 12:50-13:00 PM | Closing Remark | Dr. Matthew Ritchie |
52 |
53 |
--------------------------------------------------------------------------------
/docs/code_of_conduct.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: default
3 | ---
4 |
5 | {% include header.md %}
6 |
7 | ## Code of Conduct
8 |
9 | This code of conduct is developed for the BioC Asia 2020 conference.
10 | All conference participants must agree to adhere to this code of conduct and to Bioconductor's Project-wide Code of Conduct (available [here](https://bioconductor.org/about/code-of-conduct/)).
11 |
12 | ### Social media policy
13 |
14 | Images and content from talks, workshops, and posters may be shared
15 | publicly through social media _unless_ the presenter asks for it not
16 | to be. To avoid confusion, presentations not to be shared should be
17 | labeled "Do Not Share" on each slide, as should be posters.
18 |
19 | ### The _Bioconductor_ conference aims to provide a supportive, collegial, and harassment-free environment
20 |
21 | _Bioconductor_ is dedicated to providing a supportive, collegial, and harassment-free
22 | conference experience for everyone, regardless of:
23 | * gender, gender identity and expression, sexual orientation, disability,
24 | physical appearance, body size, race, age or religion.
25 | * intellectual position: approaches to data analysis, software preferences, coding style, scientific perspective, etc.
26 |
27 | We do not tolerate harassment, intimidation, or bullying of conference participants in talks,
28 | workshops, poster sessions, social activities,
29 | or online. Sexual language and imagery is not appropriate for any conference venue, including talks.
30 | Conference participants violating these rules may be sanctioned or expelled from the conference with no refund,
31 | at the discretion of the conference organizers. Our anti-harassment policy can be found at: http://biocasia2020.bioconductor.org/code_of_conduct
32 |
33 | ### Examples of unacceptable harassment, intimidation, and bullying behavior
34 |
35 | Harassment includes, but is not limited to:
36 |
37 | * Making comments, to an audience or personally, that belittle or demean another person
38 | * Sexual images in public spaces
39 | * Stalking or following
40 | * Harassing photography or recording
41 | * Sustained disruption of talks or other events
42 | * Inappropriate physical contact
43 | * Unwelcome sexual attention
44 | * Advocating for, or encouraging, any of the above behaviour
45 |
46 | Intimidation and bullying include, but are not limited to:
47 |
48 | * Aggressive or browbeating behavior directed at someone during a public presentation
49 | * Mocking or insulting another person's intellect, work, perspective, or question/comment
50 | * Making reference to someone's gender, gender identity and expression, sexual orientation, disability,
51 | physical appearance, body size, race, age, religion, or other personal attribute in the context of a scientific
52 | discussion
53 | * Deliberately making someone feel unwelcome
54 |
55 | ### Enforcement
56 |
57 | Participants asked to stop any harassing behavior are expected to
58 | comply immediately.
59 |
60 | If a participant engages in harassing behaviour, event organisers
61 | retain the right to take any actions to keep the event a welcoming
62 | environment for all participants. This includes warning the offender
63 | or expulsion from the conference with no refund.
64 |
65 | Event organisers may take action to redress anything designed to, or
66 | with the clear impact of, disrupting the event or making the
67 | environment hostile for any participants.
68 |
69 | We expect participants to follow these rules at all event venues and
70 | event-related social activities. We think people should follow these
71 | rules outside event activities too!
72 |
73 | ### Reporting
74 |
75 | If someone makes you or anyone else feel unsafe or unwelcome, please
76 | report it as soon as possible. Harassment and other code of conduct
77 | violations reduce the value of our event for everyone. We want you to
78 | be happy at our event. People like you make our event a better place.
79 |
80 | You can make a report either personally or anonymously.
81 |
82 | #### Anonymous or Non-anonymous Report
83 |
84 | You can make an anonymous or non-anonymous report here:
85 | https://tinyurl.com/bioccomplaint. It is a free-form text box that
86 | will be forwarded to conference organizers.
87 |
88 | We can't follow up an anonymous report with you directly, but we will
89 | fully investigate it and take whatever action is necessary to prevent
90 | a recurrence.
91 |
92 | #### Personal Report
93 |
94 | You can make a personal report with any of the conference
95 | anti-harassment committee: Jin Gu, Rui Jiang, Qian Liu, and Peter Hickey.
96 |
97 | When taking a personal report, our staff will ensure you are safe and
98 | cannot be overheard. They may involve other event staff to ensure your
99 | report is managed properly. Once safe, we'll ask you to tell us about
100 | what happened. This can be upsetting, but we'll handle it as
101 | respectfully as possible, and you can bring someone to support
102 | you. You won't be asked to confront anyone and we won't tell anyone
103 | who you are.
104 |
105 | Our team will be happy to help you contact hotel/venue security, local
106 | law enforcement, local support services, provide escorts, or otherwise
107 | assist you to feel safe for the duration of the event. We value your
108 | attendance.
109 |
110 | Conference organizers: workshop@bioconductor.org
111 | Anonymous complaints: tinyurl.com/bioccomplaint
112 |
113 | ### Anti-harassment Committee
114 |
115 | | Member | Contact |
116 | |---|---|---|
117 | | | Jin Gu <[jgu@tsinghua.edu.cn][2]> |
118 | | | Rui Jiang <[ruijiang@tsinghua.edu.cn][4]> |
119 | | | Qian Liu <[qian.liu@roswellpark.org][6]> |
120 | | | Peter Hickey <[hickey@wehi.edu.au][8]> |
121 |
122 | [0]: mailto:workshop@bioconductor.org?subject=BioC2019%20code-of-conduct
123 | [2]: mailto:jgu@tsinghua.edu.cn?subject=BioC2019%20code-of-conduct
124 | [4]: mailto:ruijiang@tsinghua.edu.cn?subject=BioC2019%20Code-of-conduct
125 | [6]: mailto:qian.liu@roswellpark.org?subject=BioC2019%20Code-of-conduct
126 | [8]: mailto:hickey@wehi.edu.au?subject=BioC2019%20Code-of-conduct
127 |
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/docs/workshops.md:
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1 | ---
2 | layout: default
3 | ---
4 |
5 | {% include header.md %}
6 |
7 | ## Workshops
8 |
9 | Join the *Bioconductor*
10 | [\#biocasia2020](https://community-bioc.slack.com/archives/CSF3EKY0Y) channel for up-to-date information.
11 |
12 | ## Getting started
13 |
14 | **Access and launch workshops by [clicking here](http://workshop.bioc.cancerdatasci.org/).**
15 |
16 | ### Chinese (中文)
17 |
18 | | Workshop | Source | Docker |
19 | | :----------------------------------------------------------------------------------------------------------------------- | :------------------------------------------------------------------------------------------------- | :---------------------------------------------------------------------------------------------------------------------- |
20 | | [使用limma、Glimma和edgeR，RNA-seq数据分析易如反掌](https://xueyidong.github.io/RNAseq123CN/) | [](https://github.com/XueyiDong/RNAseq123CN) | [](https://hub.docker.com/r/xueyidong/rnaseq123cn) |
21 | | [Analysis and visualization of microbiome datasets using MicrobiotaProcess](https://yulab-smu.top/MicrobiotaProcessWorkshop/) | [](https://github.com/YuLab-SMU/MicrobiotaProcessWorkshop) | [](https://hub.docker.com/r/xushuangbin/microbiotaprocessworkshop) |
22 | | [An introduction to single-cell RNA-sequencing analysis in Bioconductor](https://you-k.github.io/scRNA-seq-workshop/) | [](https://github.com/YOU-k/scRNA-seq-workshop) | [](https://hub.docker.com/u/chloeyou/scRNA-seq-workshop) |
23 |
24 |
25 |
26 | ### English
27 |
28 | | Workshop | Source | Docker |
29 | | :----------------------------------------------------------------------------------------------------------------------- | :------------------------------------------------------------------------------------------------- | :---------------------------------------------------------------------------------------------------------------------- |
30 | | [trackViewer: Lollipop/Dandelion plots for methylation status and mutation data](https://jianhong.github.io/trackViewerBiocAsia2020Workshop/) | [](https://github.com/jianhong/trackViewerBiocAsia2020Workshop) | [](https://hub.docker.com/r/jianhong/trackviewerbiocasia2020workshop) |
31 | | [Building a Bioconductor package](https://saskiafreytag.github.io/making_bioconductor_pkg) | [](https://github.com/SaskiaFreytag/making_bioconductor_pkg) | [](https://hub.docker.com/r/saskiafreytag/making_bioconductor_pkg) |
32 | | [Bioconductor toolchain for usage and development of reproducible bioinformatics pipelines in CWL](https://liubuntu.github.io/Bioc2020RCWL/) | [](https://github.com/Liubuntu/Bioc2020RCWL) | [](https://hub.docker.com/repository/docker/liubuntu/bioc2020rcwl) |
33 | | [tidytranscriptomics: analysing single-cell and bulk RNA sequencing data following the tidy data paradigm](https://stemangiola.github.io/biocasia2020_tidytranscriptomics/) | [](https://github.com/stemangiola/biocasia2020_tidytranscriptomics) | [](https://hub.docker.com/r/stemangiola/biocasia2020_tidytranscriptomics) |
34 | | [Hands-on experience to CiteFuse that consists of a suite of tools for the integration and the downstream analysis of CITE-seq data](https://sydneybiox.github.io/BiocAsia2020CiteFuse) | [](https://github.com/SydneyBioX/BiocAsia2020CiteFuse) | [](https://hub.docker.com/r/yingxinlin/biocasia2020citefuse) |
35 |
36 |
37 | ## Using workshop docker images locally
38 |
39 |
40 |
41 | Workshops with preinstalled dependencies can be run locally using
42 | Docker.
43 |
44 | - `docker pull
22 |
23 | 
27 |
28 |
31 | Conference Home
32 | Registration
33 | Call for submissions
34 |
35 |
42 | - Schedule
43 |
44 | - Workshops
45 |
46 | Resources
47 | - Organizing committee
48 |
49 |
50 |
51 |
52 |
53 | Code of Conduct
54 | Past conferences
55 |
58 |
59 | 
64 |
66 | Conference Sponsors 67 |
68 | 69 |
74 |
75 |
76 | 
81 |
82 |
83 | 
88 |
89 |
90 | 
95 |
96 |
97 | 
102 |
103 |
104 | 
109 |
110 |
172 |
173 | Bioconductor: https://bioconductor.org
174 | Hosted on GitHub Pages
175 | Theme by orderedlist
176 |