Managing information

Your efforts will pay off.

Reference and literature management

We assume that you have completed the first steps and you are part of the NutritionalLungImmunity Zotero group. We ask all our team members to add relevant literature to the Zotero NutritionalLungImmunity group and tag their items with a minimal set of tags. You can read about how to add Zotero tags here. Whatever tags you add will be added to the other team members tag, assuming that you are syncing your library. Please check before adding a paper if the reference is already in the library–if so, simply add tags to the existing reference.

To have the new bibliography be included on the website, you can do one of two things. You can manually export the bib file and drop it and save it as\_bibliography\references.bib, or alternatively, you can use an add-on such as better BibTex that automatically exports your bib file. Once you are ready to push your new bib file onto the website, follow these steps on how to do so. We use Jekyll Scholar to manage the reference on the webfront (hence why the standardized tags!). It allows you to include subset of literature on the website based on fields in the bibfile.

Reference tags

Tag Include if
Monocyte derived dendritic cell Related to cell type
Dendritic cell Related to cell type
Monocyte derived macrophage Related to cell type
Alveolar macrophage Related to cell type
Alveolar epithelial cell Related to cell type
Airway epithelial cell Related to cell type
Aspergillus fumigatus Related to the fungus itself
Neutrophil Related to cell type
Innate immunity Overview of innate immunity response
Software Related to software used in the project
Review paper Reference is a review paper
Invasive Pulmonary Aspergillosis Paper specific to IPA
In vitro Includes in vitro data used to calibrate a model
Multiscale modeling Reference related to techniques of multiscale modeling
Preprocessing tools Related to a tool used in the preprocessing step
Bioinformatics tool Related to a tool used in the bionformatics analysis
Our publication Papers that cite funding related to these projects
Intracellular model Paper is used in the building of an intracellular network model in this project
Parameter reference A parameter related to a model is derived from this paper
Human Includes data from humans
Mouse Includes data from mice
Numerical methods Paper related to numerical method
Software architecture Paper related to software architecture
Information management Paper related to information management
Transcriptomic dataset Paper includes a transcriptomic dataset

Our suggested Github workflow

Github and Jekyll workflow

Adding assets onto Girder

Go to our Girder instance to upload/download data. Assuming you have the appropriate permissions, you should be able to upload/download assets onto Girder. We include a brief description of some of the Girder collections to orient you, although once you go to Girder, each collection contains information that describes what is in them.

Overview of Girder collections

Girder collection (non-exhaustive list) Includes (non-exhaustively)
Model dissemination Includes project documentation, and presentation materials.
Experimental protocols and metadata associated to experiments Includes experimental protocols and experimental metadata associated with various experiments related to this project
Monocyte derived macrophages Includes all data related to monocyte derived macrophages, including wiring diagrams for model, experimental data for model validation, processing output for bioinformatics data related to the analysis of macrophages, etc. (see e.g the monocyte derived macrophage subsite to get an idea of what sort of data is associated with a monocyte derived macrophage).

Once you find the appropriate place, add the appropriate tags (#girder-asset-tags) to the asset as a markdown comment, e.g. [//]: <TAG>. This will allow you to query in girder by using these tags. For example, now you can find all posters where Bandita Adhikari is first author by typing "NLI:POSTER" "NLI:FIRSTAUTHOR:BanditaAdhikari" in the query field on Girder.

To make life easier, we made some python scripts where you can choose tags from a GUI and it will write to a file that you can copy and paste onto the information tab.

Girder asset tags

Tag Include if
NLI:POSTER Asset is a poster
NLI:DOCUMENTATION Asset is related to documentation for the project
NLI:SLIDES Asset is for a presentation in slide format
NLI:EXP.DATA Asset is part of an experiment related to the NLI project
NLI:METADATA Asset is metadata associated to a dataset
NLI:EXP.PROTOCOL Asset is metadata associated to a dataset
NLI:TRANSCRIPTOMICS Asset is related to a transcriptomic experiment
NLI:TISSUESCALE Asset is related to data at the tissue scale
NLI:INTRACELLULARSCALE Asset is related to data at the intracellular scale
NLI:RESULTS Asset presents results for an analysis or for model
NLI:ABSTRACT Asset is an abstract for a presentation
NLI:MODEL Asset is associated with the building of a model
NLI:MDMACROPHAGE Asset is associated with the cell type
NLI:MDDC Asset is associated with the cell type
NLI:ALVEOLARMACROPHAGE Asset is associated with the cell type
NLI:NEUTROPHIL Asset is associated with the cell type
NLI:ALVEOLAREPITHELIALCELL Asset is associated with the cell type
NLI:ENDOTHELIALCELL Asset is associated with the cell type
NLI:LABORATORYNOTEBOOK Asset is a laboratory notebook
NLI:LASTAUTHOR:LuisSordoVieira Last/Senior author(s)
NLI:LASTAUTHOR:ReinhardLaubenbacher Last/Senior author(s)
NLI:LASTAUTHOR:BanditaAdhikari Last/Senior author(s)
NLI:LASTAUTHOR:JosephMasison Last/Senior author(s)
NLI:LASTAUTHOR:HenriqueDeAssis Last/Senior author(s)
NLI:LASTAUTHOR:YuMei Last/Senior author(s)
NLI:LASTAUTHOR:BornaMehrad Last/Senior author(s)
NLI:LASTAUTHOR:MichaelGrauer Last/Senior author(s)
NLI:LASTAUTHOR:WilliamSchroeder Last/Senior author(s)
NLI:LASTAUTHOR:NingYang Last/Senior author(s)
NLI:LASTAUTHOR:BrianHelba Last/Senior author(s)
NLI:LASTAUTHOR:JonathanBeezley Last/Senior author(s)
NLI:FIRSTAUTHOR:LuisSordoVieira First author(s)
NLI:FIRSTAUTHOR:ReinhardLaubenbacher First author(s)
NLI:FIRSTAUTHOR:BanditaAdhikari First author(s)
NLI:FIRSTAUTHOR:JosephMasison First author(s)
NLI:FIRSTAUTHOR:HenriqueDeAssis First author(s)
NLI:FIRSTAUTHOR:YuMei First author(s)
NLI:FIRSTAUTHOR:BornaMehrad First author(s)
NLI:FIRSTAUTHOR:MichaelGrauer First author(s)
NLI:FIRSTAUTHOR:WilliamSchroeder First author(s)
NLI:FIRSTAUTHOR:NingYang First author(s)
NLI:FIRSTAUTHOR:BrianHelba First author(s)
NLI:FIRSTAUTHOR:JonathanBeezley First author(s)

That’s not all

If you feel up to the challenge, you can also write your own python scripts to upload/download data from our Girder collection. You can find the manual for Girder here.