Adding a bibliography (#1434)

* Adding bibliography

* Update style_guide.md (#1435)

---------

Co-authored-by: Korbinian Bösl <[email protected]>

Gemfile

@@ -13,6 +13,7 @@ group :jekyll_plugins do
   gem 'jekyll-github-metadata', '~> 2.15'
   gem 'jekyll-relative-links', '~> 0.6'
   gem 'jekyll-seo-tag', '~> 2.8'
+  gem 'jekyll-scholar', '~> 7.1.3'
   gem 'jekyll-remote-theme'
 end
 

_bibliography/references.bib

@@ -0,0 +1,148 @@
+@article{field2008migs,
+  title={The minimum information about a genome sequence (MIGS) specification},
+  author={Field, D. and et al.},
+  journal={Nature biotechnology},
+  volume={26},
+  number={5},
+  pages={541--547},
+  year={2008},
+  doi={10.1038/nbt1360},
+  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2409278/}
+}
+
+@article{ham2012jbeiice,
+  title={Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools},
+  author={Ham, T. S. and et al.},
+  journal={Nucleic acids research},
+  volume={40},
+  number={18},
+  pages={e141},
+  year={2012},
+  doi={10.1093/nar/gks531},
+  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467034/}
+}
+
+@article{hecht2018bacterial,
+  title={A minimum information standard for reproducing bench-scale bacterial cell growth and productivity},
+  author={Hecht, A. and et al.},
+  journal={Communications biology},
+  volume={1},
+  pages={219},
+  year={2018},
+  doi={10.1038/s42003-018-0220-6},
+  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6283831/}
+}
+
+@article{kuwahara2017sbolme,
+  title={SBOLme: a Repository of SBOL Parts for Metabolic Engineering},
+  author={Kuwahara, H. and et al.},
+  journal={ACS synthetic biology},
+  volume={6},
+  number={4},
+  pages={732--736},
+  year={2017},
+  doi={10.1021/acssynbio.6b00278},
+  url={https://pubmed.ncbi.nlm.nih.gov/28076956/}
+}
+
+@article{maloy2007strain,
+  title={Strain Collections and Genetic Nomenclature},
+  author={Maloy, S. R. and Hughes, K. T.},
+  journal={Methods in Enzymology},
+  pages={3--8},
+  year={2007},
+  doi={10.1016/s0076-6879(06)21001-2},
+  url={https://pubmed.ncbi.nlm.nih.gov/17352909/}
+}
+
+@article{parte2020lpsn,
+  title={List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ},
+  author={Parte, A. C. and et al.},
+  journal={International journal of systematic and evolutionary microbiology},
+  volume={70},
+  number={11},
+  pages={5607--5612},
+  year={2020},
+  doi={10.1099/ijsem.0.004332},
+  url={https://pubmed.ncbi.nlm.nih.gov/32701423/}
+}
+
+@article{sainzdemurieta2016toward,
+  title={Toward the First Data Acquisition Standard in Synthetic Biology},
+  author={Sainz de Murieta, I. and Bultelle, M. and Kitney, R. I.},
+  journal={ACS synthetic biology},
+  volume={5},
+  number={8},
+  pages={817--826},
+  year={2016},
+  doi={10.1021/acssynbio.5b00222},
+  url={https://pubmed.ncbi.nlm.nih.gov/26854090/}
+}
+
+@article{sarkans2018biostudies,
+  title={The BioStudies database—one stop shop for all data supporting a life sciences study},
+  author={Sarkans, U. and et al.},
+  journal={Nucleic Acids Research},
+  pages={D1266--D1270},
+  year={2018},
+  doi={10.1093/nar/gkx965},
+  url={https://pubmed.ncbi.nlm.nih.gov/29069414/}
+}
+
+@article{spidlen2021data,
+  title={Data File Standard for Flow Cytometry, Version FCS 3.2},
+  author={Spidlen, J. and et al.},
+  journal={Cytometry. Part A: the journal of the International Society for Analytical Cytology},
+  volume={99},
+  number={1},
+  pages={100--102},
+  year={2021},
+  doi={10.1002/cyto.a.24225},
+  url={https://pubmed.ncbi.nlm.nih.gov/32881398/}
+}
+
+@article{strenda2014standards,
+  title={Standards for Reporting Enzyme Data: The STRENDA Consortium: What it aims to do and why it should be helpful},
+  journal={Perspectives in Science},
+  volume={1},
+  number={1-6},
+  pages={131--137},
+  year={2014},
+  doi={10.1016/j.pisc.2014.02.012},
+  url={https://www.sciencedirect.com/science/article/pii/S2213020914000135}
+}
+
+@article{tellechealuzardo2020linking,
+  title={Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering},
+  author={Tellechea-Luzardo, J. and et al.},
+  journal={ACS synthetic biology},
+  volume={9},
+  number={3},
+  pages={536--545},
+  year={2020},
+  doi={10.1021/acssynbio.9b00400},
+  url={https://pubmed.ncbi.nlm.nih.gov/32078768/}
+}
+
+@article{tenhoopen2015m2b3,
+  title={Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards},
+  author={Ten Hoopen, P. and et al.},
+  journal={Standards in genomic sciences},
+  volume={10},
+  pages={20},
+  year={2015},
+  doi={10.1186/s40793-015-0001-5},
+  url={https://pubmed.ncbi.nlm.nih.gov/26203332/}
+}
+
+@article{zhang2017sboldesigner,
+  title={SBOLDesigner 2: An Intuitive Tool for Structural Genetic Design},
+  author={Zhang, M. and et al.},
+  journal={ACS synthetic biology},
+  volume={6},
+  number={7},
+  pages={1150--1160},
+  year={2017},
+  doi={10.1021/acssynbio.6b00275},
+  url={https://pubmed.ncbi.nlm.nih.gov/28441476/}
+}

_config.yml

@@ -135,10 +135,14 @@ defaults:
     values:
       sidebar: about
 
+scholar:
+  style: modern-language-association
+
 plugins:
   - elixir-toolkit-theme-plugins
   - jemoji
   - jekyll-redirect-from
   - jekyll-sitemap
   - jekyll-github-metadata
   - jekyll-octicons
+  - jekyll-scholar

pages/contribute/style_guide.md

@@ -42,9 +42,10 @@ In general, we follow the European Commission's [Web Writing Style Guide](https:
       * This is item 3 of the list.
   * **Numbers:** spell the numbers one to ten out. After that, write the numbers (11, 12, 13, etc.).
   * **Quotations:** use double quotes for quotations, and single quotes for quotes within quotes.
-  * **References:** use the [Nature Author instructions](https://www.nature.com/srep/author-instructions/submission-guidelines#references) for books and papers. Use "*et al.*" for more than five authors.
-    * Bellin, D. L. *et al.* Electrochemical camera chip for simultaneous imaging of multiple metabolites in biofilms. Nat. Commun. 7, 10535; [10.1038/ncomms10535](http://www.nature.com/articles/ncomms10535) (2016).
-    * Lam, J. <cite>Data Management</cite>. (John Wiley & Sons, Inc., 2019).
+  * **References:**
+    * add your citations as bibtex to the `_bibliography/references.bib` file
+    * add `{% cite reference_key %}` to the text where you are citing the reference
+    * add  `## Bibliography` `{% bibliography --cited %}` to show a bibliography section with cited refrences on a page.
   * **That/which:** use "that" when you are defining something and "which" when you are adding extra information about it e.g.:
     * "The cat that was on the table suddenly got up" is telling us which cat it was. It is important to the meaning of the sentence because you are not talking about any cat, just the cat on the table.
     * "The cat, which was sitting on the table, suddenly got up" is giving us extra information about the cat. The information is not necessary to understand the sentence. You can remove the clause and the sentence will still be clear. Clauses starting with "which" usually begin with a comma.