Merge pull request #427 from danielskatz/patch-1

changes in bib to try to fix current and future issues

Author: vsoch

paper/paper.bib

@@ -1,28 +1,13 @@
 @ARTICLE{Kurtzer2017-xj,
   title     = "Singularity: Scientific containers for mobility of compute",
   author    = "Kurtzer, Gregory M and Sochat, Vanessa and Bauer, Michael W",
-  abstract  = "Here we present Singularity, software developed to bring
-               containers and reproducibility to scientific computing. Using
-               Singularity containers, developers can work in reproducible
-               environments of their choosing and design, and these complete
-               environments can easily be copied and executed on other
-               platforms. Singularity is an open source initiative that
-               harnesses the expertise of system and software engineers and
-               researchers alike, and integrates seamlessly into common
-               workflows for both of these groups. As its primary use case,
-               Singularity brings mobility of computing to both users and HPC
-               centers, providing a secure means to capture and distribute
-               software and compute environments. This ability to create and
-               deploy reproducible environments across these centers, a
-               previously unmet need, makes Singularity a game changing
-               development for computational science.",
   journal   = "PLoS One",
   doi       = "journal.pone.0177459",
   publisher = "Public Library of Science",
   volume    =  12,
   number    =  5,
   pages     = "e0177459",
-  month     =  "11~" # may,
+  month     =  may,
   year      =  2017
 }
 
@@ -43,25 +28,6 @@ @INPROCEEDINGS{McLay2011-wu
   booktitle = "State of the Practice Reports",
   author    = "McLay, Robert and Schulz, Karl W and Barth, William L and
                Minyard, Tommy",
-  abstract  = "Commodity-based Linux HPC clusters dominate the scientific
-               computing landscape in both academia and industry ranging from
-               small research clusters to petascale supercomputers supporting
-               thousands of users. To support broad user communities and manage
-               a user-friendly environment, end-user sites must combine a range
-               of low-level system software with multiple compiler chains,
-               support libraries, and a suite of 3rd party applications. In
-               addition, large systems require bare metal provisioning and a
-               flexible software management strategy to maintain consistency
-               and upgrade-ability across thousands of compute nodes. This
-               report documents a Linux operating system framework, (LosF),
-               which has evolved over the last seven years to provide an
-               integrated strategy for the deployment of multiple HPC systems
-               at the Texas Advanced Computing Center. Documented within this
-               effort is the high-level cluster configuration options and
-               definitions, bare-metal provisioning, hierarchical HPC software
-               stack design, package-management, user environment management
-               tools, user account synchronization, and local customization
-               configurations.",
   publisher = "Association for Computing Machinery",
   number    = "Article 9",
   pages     = "1--11",
@@ -95,7 +61,7 @@ @MISC{noauthor_undated-ok
   abstract    = "Build and deploy Singularity containers to GitHub releases,
                  and pull with the singularity-hpc client -
                  singularityhub/singularity-deploy",
-  institution = "Github",
+  institution = "GitHub",
   year      =  2021
 }
 
@@ -119,8 +85,6 @@ @MISC{noauthor_undated-eh
   title       = "binoc",
   author      = "Scott, Alec",
   howpublished = "\url{https://github.com/autamus/binoc}",
-  abstract    = "Binoc is a Lookout Bot that updates containers in Autamus -
-                 autamus/binoc",
   institution = "Github",
   year        = 2021
 }
@@ -153,9 +117,9 @@ @MISC{noauthor_undated-rj
 @incollection{cook2017opinionated,
   title={The Opinionated Jupyter Stacks},
   author={Cook, Joshua},
-  booktitle={Docker for Data Science},
+  booktitle={{Docker for Data Science}},
   pages={119--135},
-  year={2017},
+  year=2017,
   publisher={Springer},
   doi="10.1007/978-1-4842-3012-1_7"
 }
@@ -177,7 +141,7 @@ @article{gorgolewski2017bids
   volume={13},
   number={3},
   pages={e1005209},
-  year={2017},
+  year=2017,
   doi="10.1371/journal.pcbi.1005209",
   publisher={Public Library of Science}
 }
@@ -190,7 +154,7 @@ @article{da2017biocontainers
   volume={33},
   number={16},
   pages={2580--2582},
-  year={2017},
+  year=2017,
   publisher={Oxford University Press}
 }
 
@@ -206,17 +170,15 @@ @MISC{noauthor_undated-kp
 @inproceedings{environment_modules,
   title={Modules: Providing a flexible user environment},
   author={Furlani, John L},
-  booktitle={Proceedings of the fifth large installation systems administration conference (LISA V)},
+  booktitle={{Proceedings of the Fifth Large Installation Systems Administration Conference (LISA V)}},
   pages={141--152},
   year={1991}
 }
 
 @Software{SRegistry,
   title        = "Singularity Registry Documentation",
-  booktitle    = "Singularity Registry Documentation",
+  booktitle    = {{Singularity Registry Documentation}},
   author       = "Sochat, Vanessa",
-  abstract     = "Background information and documentation for setting up
-                  a Singularity Registry",
   howpublished = "\url{https://singularityhub.github.io/sregistry/}",
   note         = "Accessed: 2017-9-26",
   year      =  2017
@@ -228,26 +190,6 @@ @ARTICLE{Boettiger2014-cz
   title         = "An introduction to Docker for reproducible research, with
                    examples from the {R} environment",
   author        = "Boettiger, Carl",
-  abstract      = "As computational work becomes more and more integral to many
-                   aspects of scientific research, computational
-                   reproducibility has become an issue of increasing importance
-                   to computer systems researchers and domain scientists alike.
-                   Though computational reproducibility seems more straight
-                   forward than replicating physical experiments, the complex
-                   and rapidly changing nature of computer environments makes
-                   being able to reproduce and extend such work a serious
-                   challenge. In this paper, I explore common reasons that code
-                   developed for one research project cannot be successfully
-                   executed or extended by subsequent researchers. I review
-                   current approaches to these issues, including virtual
-                   machines and workflow systems, and their limitations. I then
-                   examine how the popular emerging technology Docker combines
-                   several areas from systems research - such as operating
-                   system virtualization, cross-platform portability, modular
-                   re-usable elements, versioning, and a `DevOps' philosophy,
-                   to address these challenges. I illustrate this with several
-                   examples of Docker use with a focus on the R statistical
-                   environment.",
   month         =  oct,
   year          =  2014,
   archivePrefix = "arXiv",
@@ -260,22 +202,6 @@ @ARTICLE{Santana-Perez2015-wo
   title     = "Towards Reproducibility in Scientific Workflows: An
                {Infrastructure-Based} Approach",
   author    = "Santana-Perez, Idafen and P{\'e}rez-Hern{\'a}ndez, Mar{\'\i}a S",
-  abstract  = "It is commonly agreed that in silico scientific experiments
-               should be executable and repeatable processes. Most of the
-               current approaches for computational experiment conservation and
-               reproducibility have focused so far on two of the main
-               components of the experiment, namely, data and method. In this
-               paper, we propose a new approach that addresses the third
-               cornerstone of experimental reproducibility: the equipment. This
-               work focuses on the equipment of a computational experiment,
-               that is, the set of software and hardware components that are
-               involved in the execution of a scientific workflow. In order to
-               demonstrate the feasibility of our proposal, we describe a use
-               case scenario on the Text Analytics domain and the application
-               of our approach to it. From the original workflow, we document
-               its execution environment, by means of a set of semantic models
-               and a catalogue of resources, and generate an equivalent
-               infrastructure for reexecuting it.",
   journal   = "Sci. Program.",
   publisher = "Hindawi Publishing Corporation",
   volume    =  2015,
@@ -288,17 +214,6 @@ @ARTICLE{Wandell2015-yt
   title         = "Data management to support reproducible research",
   author        = "Wandell, B A and Rokem, A and Perry, L M and Schaefer, G and
                    Dougherty, R F",
-  abstract      = "We describe the current state and future plans for a set of
-                   tools for scientific data management (SDM) designed to
-                   support scientific transparency and reproducible research.
-                   SDM has been in active use at our MRI Center for more than
-                   two years. We designed the system to be used from the
-                   beginning of a research project, which contrasts with
-                   conventional end-state databases that accept data as a
-                   project concludes. A number of benefits accrue from using
-                   scientific data management tools early and throughout the
-                   project, including data integrity as well as reuse of the
-                   data and of computational methods.",
   month         =  feb,
   year          =  2015,
   archivePrefix = "arXiv",