Edit me to practice contributing to a collaborative Manubot manuscript

test edit - hello world. This manuscript (permalink) was automatically generated from manubot/try-manubot@c320824 on November 8, 2024.

Authors

✉ — Correspondence possible via GitHub Issues or email to Jane Roe <jane.roe@whatever.edu>.

Abstract

Manubot is an open source tool for writing manuscripts on GitHub in markdown format. Manubot applies the git-based software workflow to scholarly writing, enabling enhanced transparency, collaboration, automation, and reproducibility.

This manuscript is a Manubot demo, intended to give users a playground to practice using Manubot. Everyone is encouraged to try writing with Manubot by editing this manuscript.

Manubot is described in the paper titled “Open collaborative writing with Manubot” [1].

Main text

Lorem ipsum text [2] is a strong introduction for any manuscript.

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

Manubot makes it easy to cite this manuscript [3]. It has been used to write several manuscripts that are now preprints on bioRxiv [4,5,6,7]. Notice that only [6] has the correct name of the preprint server. Manubot allows authors to overwrite reference information, in this case with a BibTeX file.

Lorem ipsum also makes a strong conclusion [8] here is another reference to see if duplicate references are picked up by the program if the second author uses a different identifier for the same reference like here with the immediately preceding reference [9]. Did it work?

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

I’m wondering about how editing this file works within the web browser.

Testing inserting a reference Note that some buffers can potentially introduce modifications onto proteins such as carbamylation from urea at high temperatures [10,11] .

Trying with references again [12]

The objectives of the action plan for each sector are as follows:

Development sector Specific objectives of action plan
Agriculture SO 1: Recuperate and restore the fertility of degraded land
SO 2: Improve access for farmers to high quality agricultural production factors (equipment, inputs, land, results of agricultural research etc.)
SO 3: Improve the resilience of stakeholders to climate change}
SO 4: Develop early warning systems to ensure efficient management of climate variability and change
Animal production SO 1: Improve the security of pastoral activities through better dissemination and exploitation of information on pastoral resources and associated access
SO 2: Ensure the security of animal capital with a view to supporting the pastoral economy on a sustainable basis and improve the resilience of stakeholders in order to achieve sustainable food security in Burkina Faso
SO 3: Reduce the vulnerability of farmers to climate change and contribute to local economic development
Environment and natural resources SO 1: Increase productivity and the resilience of ecosystems
SO 2: Improve biodiversity conservation
SO 3: Improve research and ecological monitoring
SO 4: Reduce GG emissions
Energy SO 1: Reduce the impact of climate change on the energy sector
SO 2: Ensure a sustainable supply of energy for cooking
SO 3: Reduce electricity consumption
SO 4: Gain more knowledge into the impact of climate change on the energy sector
Health SO 1: Ensure leadership and governance in terms of adapting to the impacts of climate change on the health sector
SO 2: Increase human resources in the health sector skilled in adapting to the effects of climate change
SO 3: Improve the early warning system and the response to climate change-related phenomena
SO 4: Adapt health infrastructure to the effects of climate change
SO 5: Improve research in the field of climate change
Infrastructure and housing OS 1: Promote access to decent accommodation for disadvantaged social groups by providing rental accommodation, supporting DIY construction and building social housing stock
SO 2: Provide public facilities and road, water and rain and waste-water drainage infrastructure which is practical and resilient through good design/implementation and good maintenance
OS 3:Turn the towns of Burkina Faso into hubs of economic growth and sustainable development by promoting a green economy
Horizontal issues SO 1: Help to improve mastery of environmental problems and climate change by members of women's associations
SO 2: Help to improve the resilience of members of women's associations by implementing revenue-generating activities
SO 3: Develop adaptation technologies which take account of the conditions in women's associations on the basis of traditional knowledge
SO 4: Improve the contribution of NGOs to better governance in implementing the NAP/CC in Burkina Faso
SO 5: Ensure the sustainability of civil society initiatives in climate change adaptation
SO 6: Help to improve public involvement in the process of reflection, analysis and decision-making in connection with climate change adaptation by producing, disseminating and making efficient use of information originating from innovative CSO experiences.
SO 7:Improve the mobilisation and exploitation of water resources* *
SO 8: Improve conservation and protection of water resources
SO 9: Improve knowledge about (surface and, more importantly, underground) water resources in the context of climate change
SO 10: Improve access to sanitation

The global NAP for the country as a whole can be summarised as follows:

ADAPTATION OBJECTIVES: Protect accelerated growth pillars ADAPTATION MEASURES AT SHORT, MEDIUM AND LONG-TERM
Agriculture - Cultivate early varieties or drought-resistant crops (Short) - Apply water and soil conservation methods (stone barriers, small dikes, filtering dikes, terraces, half moons, agroforestry, dune fixing etc.) (Short) - Promote sustainable land management (SLM) (Medium) - Improve access to climate information (Medium) - Introduce agricultural insurance (Long)
Livestock farming - Fight bush fires in order to prevent destruction [13] of dry-season grazing reserves- Adopt best animal husbandry and pastoral practices (pastoral hydraulics, pastoral resource management, pasture mowing and conservation, pasture crops, silage, animal mobility and transhumance etc.) - Ensure stakeholders take account of climate variability in development project and programme planning by improving their skills - Preserve cattle breeding at serious risk from climate variability - Ensure farmers adopt animal production methods adapted to a hot climate

I wonder what happens if I do hto

Great Idea!

Testing some identifier types [14] and [15] and [16]

References

1.
Open collaborative writing with Manubot
Daniel S Himmelstein, Vincent Rubinetti, David R Slochower, Dongbo Hu, Venkat S Malladi, Casey S Greene, Anthony Gitter
Manubot (2020-05-25) https://greenelab.github.io/meta-review/
2.
3.
Edit me to practice contributing to a collaborative Manubot manuscript
John Doe, Jane Roe
Manubot (2024-10-30) https://manubot.github.io/try-manubot/
4.
GimmeMotifs: an analysis framework for transcription factor motif analysis
Niklas Bruse, Simon J van Heeringen
Cold Spring Harbor Laboratory (2018-11-20) https://doi.org/gfxrkc
5.
Plasmids for independently tunable, low-noise expression of two genes
João PN Silva, Soraia Vidigal Lopes, Diogo J Grilo, Zach Hensel
Cold Spring Harbor Laboratory (2019-01-09) https://doi.org/gfs47c
6.
Scaling tree-based automated machine learning to biomedical big data with a dataset selector
Trang T Le, Weixuan Fu, Jason H Moore
bioRxiv (2018-12) https://www.biorxiv.org/content/10.1101/502484v1
7.
Genotyping structural variants in pangenome graphs using the vg toolkit
Glenn Hickey, David Heller, Jean Monlong, Jonas A Sibbesen, Jouni Sirén, Jordan Eizenga, Eric T Dawson, Erik Garrison, Adam M Novak, Benedict Paten
Cold Spring Harbor Laboratory (2019-06-01) https://doi.org/gf3jfm
8.
Hypothermic machine perfusion in kidney transplantation.
Julie De Deken, Peri Kocabayoglu, Cyril Moers
Current opinion in organ transplantation (2016-06) https://www.ncbi.nlm.nih.gov/pubmed/26945319
9.
Hypothermic machine perfusion in kidney transplantation
Julie De Deken, Peri Kocabayoglu, Cyril Moers
Current Opinion in Organ Transplantation (2016-06) https://doi.org/f8mswg
10.
Inhibition of protein carbamylation in urea solution using ammonium-containing buffers
Shisheng Sun, Jian-Ying Zhou, Weiming Yang, Hui Zhang
Analytical Biochemistry (2014-02) https://doi.org/f5pjdg
11.
Pandora box of BCA assay. Investigation of the accuracy and linearity of the microplate bicinchoninic protein assay: Analytical challenges and method modifications to minimize systematic errors
Eduard Rogatsky
Analytical Biochemistry (2021-10) https://doi.org/gpvbj4
12.
Inhibition of protein carbamylation in urea solution using ammonium-containing buffers.
Shisheng Sun, Jian-Ying Zhou, Weiming Yang, Hui Zhang
Analytical biochemistry (2013-10-23) https://www.ncbi.nlm.nih.gov/pubmed/24161613
13.
A primer on leading the improvement of systems
DM Berwick
BMJ (1996-03-09) https://doi.org/ddjp63
14.
Gordonia otitidis NBRC 100426 (ID 76513) - BioProject - NCBI https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJDB3
15.
16.