1. Docker%20Hub, %5Curlhttps://hub.docker.com/, Accessed:%202015-11-4
2. BioContainers:%20an%20open-source%20and%20community-driven%20framework%20for%20software%20standardization, da%20Veiga%20Leprevost,%20Felipe%20and%20Gr%C3%BCning,%20Bj%C3%B6rn%20A%20and%20Alves%20Aflitos,%20Saulo%20and%20R%C3%B6st,%20Hannes%20L%20and%20Uszkoreit,%20Julian%20and%20Barsnes,%20Harald%20and%20Vaudel,%20Marc%20and%20Moreno,%20Pablo%20and%20Gatto,%20Laurent%20and%20Weber,%20Jonas%20and%20Bai,%20Mingze%20and%20Jimenez,%20Rafael%20C%20and%20Sachsenberg,%20Timo%20and%20Pfeuffer,%20Julianus%20and%20Vera%20Alvarez,%20Roberto%20and%20Griss,%20Johannes%20and%20Nesvizhskii,%20Alexey%20I%20and%20Perez-Riverol,%20Yasset, Motivation:%20BioContainers%20(biocontainers.pro)%20is%20an%20open-source%20and%20community-driven%20framework%20which%20provides%20platform%20independent%20executable%20environments%20for%20bioinformatics%20software.%20BioContainers%20allows%20labs%20of%20all%20sizes%20to%20easily%20install%20bioinformatics%20software,%20maintain%20multiple%20versions%20of%20the%20same%20software%20and%20combine%20tools%20into%20powerful%20analysis%20pipelines.%20BioContainers%20is%20based%20on%20popular%20open-source%20projects%20Docker%20and%20rkt%20frameworks,%20that%20allow%20software%20to%20be%20installed%20and%20executed%20under%20an%20isolated%20and%20controlled%20environment.%20Also,%20it%20provides%20infrastructure%20and%20basic%20guidelines%20to%20create,%20manage%20and%20distribute%20bioinformatics%20containers%20with%20a%20special%20focus%20on%20omics%20technologies.%20These%20containers%20can%20be%20integrated%20into%20more%20comprehensive%20bioinformatics%20pipelines%20and%20different%20architectures%20(local%20desktop,%20cloud%20environments%20or%20HPC%20clusters).%20Availability%20and%20Implementation:%20The%20software%20is%20freely%20available%20at%20github.com/BioContainers/.%20Contact:%20yperez@ebi.ac.uk., Bioinformatics, 33, 16, 2580%E2%80%932582, aug, 2017, en, 8
3. GitHub%20Pages, Websites%20for%20you%20and%20your%20projects,%20hosted%20directly%20from%20your%20GitHub%20repository.%20Just%20edit,%20push,%20and%20your%20changes%20are%20live., Github
4. Git%20can%20facilitate%20greater%20reproducibility%20and%20increased%20transparency%20in%20science, Ram,%20Karthik, Environmental%20Science,%20Policy,%20and%20Management,%20University%20of%20California,%20Berkeley,%20Berkeley,%20CA%2094720,%20USA.%20karthik.ram@berkeley.edu., BACKGROUND:%20Reproducibility%20is%20the%20hallmark%20of%20good%20science.%20Maintaining%20a%20high%20degree%20of%20transparency%20in%20scientific%20reporting%20is%20essential%20not%20just%20for%20gaining%20trust%20and%20credibility%20within%20the%20scientific%20community%20but%20also%20for%20facilitating%20the%20development%20of%20new%20ideas.%20Sharing%20data%20and%20computer%20code%20associated%20with%20publications%20is%20becoming%20increasingly%20common,%20motivated%20partly%20in%20response%20to%20data%20deposition%20requirements%20from%20journals%20and%20mandates%20from%20funders.%20Despite%20this%20increase%20in%20transparency,%20it%20is%20still%20difficult%20to%20reproduce%20or%20build%20upon%20the%20findings%20of%20most%20scientific%20publications%20without%20access%20to%20a%20more%20complete%20workflow.%20FINDINGS:%20Version%20control%20systems%20(VCS),%20which%20have%20long%20been%20used%20to%20maintain%20code%20repositories%20in%20the%20software%20industry,%20are%20now%20finding%20new%20applications%20in%20science.%20One%20such%20open%20source%20VCS,%20Git,%20provides%20a%20lightweight%20yet%20robust%20framework%20that%20is%20ideal%20for%20managing%20the%20full%20suite%20of%20research%20outputs%20such%20as%20datasets,%20statistical%20code,%20figures,%20lab%20notes,%20and%20manuscripts.%20For%20individual%20researchers,%20Git%20provides%20a%20powerful%20way%20to%20track%20and%20compare%20versions,%20retrace%20errors,%20explore%20new%20approaches%20in%20a%20structured%20manner,%20while%20maintaining%20a%20full%20audit%20trail.%20For%20larger%20collaborative%20efforts,%20Git%20and%20Git%20hosting%20services%20make%20it%20possible%20for%20everyone%20to%20work%20asynchronously%20and%20merge%20their%20contributions%20at%20any%20time,%20all%20the%20while%20maintaining%20a%20complete%20authorship%20trail.%20In%20this%20paper%20I%20provide%20an%20overview%20of%20Git%20along%20with%20use-cases%20that%20highlight%20how%20this%20tool%20can%20be%20leveraged%20to%20make%20science%20more%20reproducible%20and%20transparent,%20foster%20new%20collaborations,%20and%20support%20novel%20uses., Source%20Code%20Biol.%20Med., 8, 1, 7, feb, 2013, en, 2
5. Enhancing%20reproducibility%20in%20scientific%20computing:%20Metrics%20and%20registry%20for%20Singularity%20containers, Sochat,%20Vanessa%20V%20and%20Prybol,%20Cameron%20J%20and%20Kurtzer,%20Gregory%20M, Here%20we%20present%20Singularity%20Hub,%20a%20framework%20to%20build%20and%20deploy%20Singularity%20containers%20for%20mobility%20of%20compute,%20and%20the%20singularity-python%20software%20with%20novel%20metrics%20for%20assessing%20reproducibility%20of%20such%20containers.%20Singularity%20containers%20make%20it%20possible%20for%20scientists%20and%20developers%20to%20package%20reproducible%20software,%20and%20Singularity%20Hub%20adds%20automation%20to%20this%20workflow%20by%20building,%20capturing%20metadata%20for,%20visualizing,%20and%20serving%20containers%20programmatically.%20Our%20novel%20metrics,%20based%20on%20custom%20filters%20of%20content%20hashes%20of%20container%20contents,%20allow%20for%20comparison%20of%20an%20entire%20container,%20including%20operating%20system,%20custom%20software,%20and%20metadata.%20First%20we%20will%20review%20Singularity%20Hub%E2%80%99s%20primary%20use%20cases%20and%20how%20the%20infrastructure%20has%20been%20designed%20to%20support%20modern,%20common%20workflows.%20Next,%20we%20conduct%20three%20analyses%20to%20demonstrate%20build%20consistency,%20reproducibility%20metric%20and%20performance%20and%20interpretability,%20and%20potential%20for%20discovery.%20This%20is%20the%20first%20effort%20to%20demonstrate%20a%20rigorous%20assessment%20of%20measurable%20similarity%20between%20containers%20and%20operating%20systems.%20We%20provide%20these%20capabilities%20within%20Singularity%20Hub,%20as%20well%20as%20the%20source%20software%20singularity-python%20that%20provides%20the%20underlying%20functionality.%20Singularity%20Hub%20is%20available%20at%20https://singularity-hub.org,%20and%20we%20are%20excited%20to%20provide%20it%20as%20an%20openly%20available%20platform%20for%20building,%20and%20deploying%20scientific%20containers., PLoS%20One, 12, 11, e0188511, nov, 2017, en, 11