CaPPA - The Catalysis Preprint Archive 
1 About CaPPA
The Catalysis Preprint Archive provides access to preprints of published papers in the field of catalysis. The goal is to provide a curated, aggregated repository of the preprints, associated data, and code, as prepared by the authors. We aim to make sharing our work and data as easy as possible. CaPPA supports aggregation of preprint repositories from GitHub, GitLab, bitbucket, and arbitrary git servers. We also can aggregate from publicly visible bazaar (bzr), mercurial (hg), subversion (svn), cvs, darcs, and fossil repositories. We can aggregate from Zenodo and FigShare, as well as Dropbox and Google Drive. We can aggregate from any zip-file that is publicly accessible by a URL. If you make your preprint available somehow, we can probably aggregate it.
This project is in the pre-alpha stage of development. It will probably change a lot as it develops. See the Roadmap for directions we are interested in considering.
2 Available preprints
Each link below will take you to the preprint page, which has more information about the preprint.
| Preprint | DOI | Repo | Citation |
|---|---|---|---|
| kitchingroup-9 | doi | Kitchin, J. R. and Nørskov, J. K. and Barteau, M. A. and Chen, J. G., "Role of Strain and Ligand Effects in the Modification of the Electronic and Chemical Properties of Bimetallic Surfaces", Physical Review Letters, 93:156801 (2004) | |
| kitchingroup-7 | doi | Kitchin, J. R. and Nørskov, J. K. and Barteau, M. A. and Chen, J. G., "Modification of the Surface Electronic and Chemical Properties of {Pt}(111) By Subsurface 3d Transition Metals", Journal of Chemical Physics, 120:10240-10246 (2004) | |
| kitchingroup-62 | doi | Alexander P. Hallenbeck and Adefemi Egbebi and Kevin P. Resnik and David Hopkinson and Shelley L. Anna and John R. Kitchin, "Comparative Microfluidic Screening of Amino Acid Salt Solutions for Post-Combustion \ce{CO2} Capture", International Journal of Greenhouse Gas Control , 43:189 - 197 (2015) | |
| kitchingroup-60 | doi | Hari Thirumalai and John R. Kitchin, "The Role of Vdw Interactions in Coverage Dependent Adsorption Energies of Atomic Adsorbates on Pt(111) and Pd(111)", Surface Science , : - (2015) | |
| kitchingroup-58 | doi | Matthew Curnan and John R. Kitchin, "Investigating the Energetic Ordering of Stable and Metastable TiO\(_2\) Polymorphs Using DFT+U and Hybrid Functionals", The Journal of Physical Chemistry C, 119: (2015) | |
| kitchingroup-57 | doi | Kitchin, John R., "Examples of Effective Data Sharing in Scientific Publishing", ACS Catalysis, 5:3894-3899 (2015) | |
| kitchingroup-56 | doi | John R. Kitchin, "Data Sharing in Surface Science", Surface Science , N/A:in press (2015) | |
| kitchingroup-55 | doi | John D. Michael and Ethan L. Demeter and Steven M. Illes and Qingqi Fan and Jacob R. Boes and John R. Kitchin, "Alkaline Electrolyte and Fe Impurity Effects on the Performance and Active-Phase Structure of {NiOOH} Thin Films for {OER} Catalysis Applications", J. Phys. Chem. C, 119:11475-11481 (2015) | |
| kitchingroup-53 | doi | Xu, Zhongnan and Joshi, Yogesh V. and Raman, Sumathy and Kitchin, John R., "Accurate Electronic and Chemical Properties of 3d Transition Metal Oxides Using a Calculated Linear Response {U} and a {DFT + U(V)} Method", The Journal of Chemical Physics, 142:144701 (2015) | |
| kitchingroup-52 | doi | Zhongnan Xu and John R. Kitchin, "Relationships Between the Surface Electronic and Chemical Properties of Doped 4d and 5d Late Transition Metal Dioxides", The Journal of Chemical Physics, 142:104703 (2015) | |
| kitchingroup-51 | doi | Jacob R. Boes and Peter Kondratyuk and Chunrong Yin and James B. Miller and Andrew J. Gellman and John R. Kitchin, "Core Level Shifts in {Cu-Pd} Alloys As a Function of Bulk Composition and Structure", Surface Science, 640:127-132 (2015) | |
| kitchingroup-50 | doi | Xu, Zhongnan and Rossmeisl, Jan and Kitchin, John R., "A Linear Response {DFT}+{U} Study of Trends in the Oxygen Evolution Activity of Transition Metal Rutile Dioxides", The Journal of Physical Chemistry C, 119:4827-4833 (2015) | |
| kitchingroup-48 | doi | Curnan, Matthew T. and Kitchin, John R., "Effects of Concentration, Crystal Structure, Magnetism, and Electronic Structure Method on First-Principles Oxygen Vacancy Formation Energy Trends in Perovskites", The Journal of Physical Chemistry C, 118:28776-28790 (2014) | |
| kitchingroup-47 | doi | Zhongnan Xu and John R. Kitchin, "Probing the Coverage Dependence of Site and Adsorbate Configurational Correlations on (111) Surfaces of Late Transition Metals", J. Phys. Chem. C, 118:25597-25602 (2014) | |
| kitchingroup-46 | doi | Ethan L. Demeter and Shayna L. Hilburg and Newell R. Washburn and Terrence J. Collins and John R. Kitchin, "Electrocatalytic Oxygen Evolution With an Immobilized {TAML} Activator", J. Am. Chem. Soc., 136:5603-5606 (2014) | |
| kitchingroup-44 | doi | Prateek Mehta and Paul A. Salvador and John R. Kitchin, "Identifying Potential \ce{BO2} Oxide Polymorphs for Epitaxial Growth Candidates", ACS Appl. Mater. Interfaces, 6:3630-3639 (2015) | |
| kitchingroup-43 | doi | Spencer D. Miller and Vladimir V. Pushkarev and Andrew J. Gellman and John R. Kitchin, "Simulating Temperature Programmed Desorption of Oxygen on {P}t(111) Using {DFT} Derived Coverage Dependent Desorption Barriers", Topics in Catalysis, 57:106-117 (2014) | |
| kitchingroup-29 | doi | Inoglu, Nilay and Kitchin, John R., "Identification of Sulfur-Tolerant Bimetallic Surfaces Using {DFT} Parametrized Models and Atomistic Thermodynamics", ACS Catalysis, :399–407 (2011) | |
| cappa |
3 Install CaPPA in Emacs
To access the CaPPA archive in Emacs add this to an init file.
(add-to-list 'package-archives
'("CaPPA" . "http://catalysis-preprint-archive.github.io/preprints/") t)
Then, you can install the `cappa' package and preprints using the Emacs package installer.
Use the `cappa' command to list the installed preprints, and preprints available for installation through Emacs. This is a work in progress.
4 Submitting a preprint
The basic process to submit a preprint to CaPPA is to create a preprint repository somewhere (the best places are gitHUB, bitbucket, or gitLAB). Your repository needs to have a file named preprint-label.el, see https://github.com/KitchinHUB/kitchingroup-9/blob/master/kitchingroup-9.el for an example.
Then send a recipe to John Kitchin (jkitchin@andrew.cmu.edu). A recipe looks like this:
(kitchingroup-9
:fetcher github
:repo "KitchinHUB/kitchingroup-9"
:files ("*"))
It has a unique preprint label, and some details that are used to convert your repo into a package.
You can see other recipes here: https://github.com/Catalysis-Preprint-Archive/melpa/tree/cappa/recipes
5 FAQ
5.1 Are there any limitations to CaPPA?
We leverage GitHUB, which has some restrictions on file sizes. For example, the package representing your preprint cannot exceed 100 MB. It is not essential to include all your data in CaPPA, as the data is available through your repository. CaPPA serves as an aggregator at this point.
For very large datasets, it probably makes sense to host them on Zenodo or Figshare, and register your preprint here with directions in it on how to access the datasets. See https://github.com/KitchinHUB/kitchingroup-50 for an example that uses Zenodo to share about 1.8 GB of computational data. See https://github.com/Catalysis-Preprint-Archive/melpa/blob/cappa/recipes/kitchingroup-55 for an example recipe that only shares the manuscript and supporting information through CaPPA, but makes the data available in the GitHUB repo and via Zenodo.
5.2 What should I share in my preprint repo?
Anything you want.
5.3 Do I have use LaTeX?
No. See http://catalysis-preprint-archive.github.io/preprints/kitchingroup-46-20160131.1840.html for an example using a Word Document. It is also possible to simply share the pdf version if that is what you want.
5.4 Do I have to use GitHUB?
No. In principle we can pull preprints from any place MELPA supports. See https://github.com/milkypostman/melpa#recipe-format. At the time of this writing, that included git, github, gitlab, bitbucket, bazaar (bzr), mercurial (hg), subversion (svn), cvs, darcs, and fossil.
- See https://zenodo.org/record/45499 for an example of using Zenodo for a preprint.
- See https://gitlab.com/jkitchin/kitchingroup-47 for a gitlab example
- See https://bitbucket.org/jkitchin/kitchingroup-44 for a bitbucket (using git) example
- See https://bitbucket.org/jkitchin/kitchingroup-48 for a bitbucket (using hg) example
- See https://www.dropbox.com/sh/ci6b2fq76th2vqr/AABduyYxnFFJ2uO1HJrp50FEa?dl=1 for an example using Dropbox.
In order of preference:
- GitHUB, Gitlab, bitbucket
- Zenodo, Figshare (these are not flexible at modifying the contents, so if you make mistakes setting up the preprint it is more difficult to fix.)
- Dropbox, Google Drive (these do not offer the version control that others offer)
6 Interested in developing?
6.1 User experience
If you can contribute ideas on how to make this work well, they are welcome.
6.2 Web interface to CaPPA
I can always use help making the Web interface better.
6.3 Alternate interfaces to CaPPA
You can access data about the archives here ./archive.json and the recipes at ./recipes.json. You can build a library in Python or Ruby to access everything from those I think. Let me know if you do that or want help doing it.
Here is a typical entry for the archive.json file
"label":{"ver":[major,minor],"deps":null,"desc":"Some descriptive text","type":"tar","props":{"authors":{"John Kitchin":"jkitchin@andrew.cmu.edu"},"maintainer":{"John Kitchin":"jkitchin@andrew.cmu.edu"}}}
"kitchingroup-9":{"ver":[20160131,1150],"deps":null,"desc":"preprint","type":"tar","props":{"authors":{"John Kitchin":"jkitchin@andrew.cmu.edu"},"maintainer":{"John Kitchin":"jkitchin@andrew.cmu.edu"}}}
Preprints as tar archive files in /preprints/label-major.minor.tar.
A typical recipe entry is:
"kitchingroup-9":{"fetcher":"github","repo":"KitchinHUB/kitchingroup-9","files":["*"]}
6.4 Roadmap
6.4.1 Analytics on downloads
Eventually we need to be able to see what preprints have been downloaded or accessed. One of our hypotheses is the availability of preprints will improve the visibility and citations of the papers. I view this as a high priority. I currently have Google Analytics setup for CaPPA.
6.4.2 Better metadata on preprints
This could be useful to find preprints funded by a grant, or by authors, or by keywords etc…
6.4.3 Alternative packaging formats
Right now we leverage the Emacs package format because the framework exists, and it is really useful. Alternative package formats might have benefits too, e.g. as a Python package or Ruby gem. Probably these can all be built from one recipe if the metadata is available to construct the required files.
6.4.4 Search
At the moment, we use a google search widget, which does not seem to be able to find anything.
6.4.5 Sortable preprint table
Eventually we hope there are hundreds of preprints in CaPPA. At that point being able to filter/search the table will be necessary to help find things.
6.4.6 Consider moving to a static server
CaPPA is hosted on GitHUB now. This has some advantages, like reliability, and collaborative maintenance. It may be incompatible with the analytics though, and it does limit the file size of a file to 100 MB, which does not allow arbitary data to be stored in CaPPA.
7 Acknowledgements
CaPPA is built on the shoulders of MELPA.