update paper to use semicolons to separate references

Signed-off-by: vsoch <[email protected]>

Author: vsoch

paper/paper.md

@@ -25,15 +25,15 @@ bibliography: paper.bib
 
 Portability and reproducibility of complex software stacks is essential for researchers to perform their work. High Performance Computing (HPC) environments add another level of complexity, where possibly conflicting dependencies must co-exist. Although container technologies like Singularity [@Kurtzer2017-xj] make it possible to "bring your own environment," without any form of central strategy to manage containers, researchers that seek reproducibility via using containers are tasked with managing their own container collection, often not taking care to ensure that a particular digest or version is used. The reproducibility of the work is at risk, as they cannot easily install and use containers, nor can they share their software with others.
 
-Singularity Registry HPC (shpc) is the first of its kind to provide an easy means for a researcher to add their research software for sharing and collaboration with other researchers to an existing collection of over 200 popular scientific libraries [@da2017biocontainers, @noauthor_undated-kp, @gorgolewski2017bids, @gamblin2015spack, @autamus]. The software installs these containers as environment modules [@McLay2011-wu] that are easy to use and read documentation for, and exposes aliases for commands in the container that the researcher can add to his or her pipeline without thinking about complex interactions with a container. The simple addition of an entry to the registry maintained by shpc comes down to adding a yaml file, and after doing this, another researcher can easily install the same software, down to the digest, to reproduce the original work.
+Singularity Registry HPC (shpc) is the first of its kind to provide an easy means for a researcher to add their research software for sharing and collaboration with other researchers to an existing collection of over 200 popular scientific libraries [@da2017biocontainers; @noauthor_undated-kp, @gorgolewski2017bids; @gamblin2015spack; @autamus]. The software installs these containers as environment modules [@McLay2011-wu] that are easy to use and read documentation for, and exposes aliases for commands in the container that the researcher can add to his or her pipeline without thinking about complex interactions with a container. The simple addition of an entry to the registry maintained by shpc comes down to adding a yaml file, and after doing this, another researcher can easily install the same software, down to the digest, to reproduce the original work.
 
 
 ## Background
 
 Using environment modules [@McLay2011-wu] on HPC clusters is a common
 trend. Although writing the recipes can be complex, it's a fairly common practice for cluster administrators to provide
-a set of natively installed recipes for their users [@noauthor_undated-bt], or for researchers to develop and deploy their own software via containers. Even well-known package managers like Spack [@noauthor_undated-ae] and EasyBuild [@noauthor_undated-dj] expose software as modules. However, these package manager approaches don't always ensure reproducibility, or ease of development for the researcher. They typically require relying on some subset of system software, the underlying operating system, or even making changes to the system, which is not under the researcher's control. Although using containers in this context has been discussed previously [@noauthor_undated-rj, @noauthor_undated-rc], the majority of these approaches and tools do not make the process of developing and installing container modules easy. The single researcher must either convince a cluster administrator to install dependencies needed for their software, or build a container and manually move and interact with it on the cluster. All of these small challenges come together to make it harder for a researcher to develop and manage their own software, and subsequently to share their approach to reproduce the work. Using Singularity containers installed via Singularity Registry HPC offers a solution to this challenge. The only requirement is the Singularity software, and writing a simple configuration file for the registry. By clearly defining commands, and pinning exact versions of scientific software, researchers on high performance computing
-clusters can have more confidence in the reproducibility of their work [@Santana-Perez2015-wo, @Boettiger2014-cz, @Wandell2015-yt].
+a set of natively installed recipes for their users [@noauthor_undated-bt], or for researchers to develop and deploy their own software via containers. Even well-known package managers like Spack [@noauthor_undated-ae] and EasyBuild [@noauthor_undated-dj] expose software as modules. However, these package manager approaches don't always ensure reproducibility, or ease of development for the researcher. They typically require relying on some subset of system software, the underlying operating system, or even making changes to the system, which is not under the researcher's control. Although using containers in this context has been discussed previously [@noauthor_undated-rj; @noauthor_undated-rc], the majority of these approaches and tools do not make the process of developing and installing container modules easy. The single researcher must either convince a cluster administrator to install dependencies needed for their software, or build a container and manually move and interact with it on the cluster. All of these small challenges come together to make it harder for a researcher to develop and manage their own software, and subsequently to share their approach to reproduce the work. Using Singularity containers installed via Singularity Registry HPC offers a solution to this challenge. The only requirement is the Singularity software, and writing a simple configuration file for the registry. By clearly defining commands, and pinning exact versions of scientific software, researchers on high performance computing
+clusters can have more confidence in the reproducibility of their work [@Santana-Perez2015-wo; @Boettiger2014-cz; @Wandell2015-yt].
 
 ## Usage