Reference health
Scalable Workflows and Reproducible Data Analysis for Genomics
23/23 checkable references clean · checked 2026-07-14
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a publisher retraction, withdrawal, or removal notice.
24 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 23 checked references that resolve
resolves10.1371/journal.pcbi.1000069
A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation
resolves10.1186/1471-2105-15-S14-S7
Community-driven development for computational biology at Sprints, Hackathons and Codefests
resolves10.1038/msb.2011.75
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
resolves10.1093/nar/gkl315
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
resolves10.1101/207092
Bioconda: A sustainable and comprehensive software distribution for the life sciences
resolves10.1038/nature08358
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans
resolves10.1093/gbe/evp012
Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment
The 24 references without a DOI — listed, not checked
no DOI — not checkedYang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13(5):555–556
no DOI — not checkedLeipzig J (2017) A review of bioinformatic pipeline frameworks. Brief Bioinform 18(3):530–536
no DOI — not checkedJeffrey D, Sanjay G (2004) Mapreduce: simplified data processing on large clusters
no DOI — not checkedWhite T (2009) Hadoop: the definitive guide, 1st edn. O’Reilly, Sebastopol, CA
no DOI — not checked(2009) Slurm workload manager.
https://slurm.schedmd.com
no DOI — not checkedStamatakis A, Ott M (2008) Exploiting fine-grained parallelism in the phylogenetic likelihood function with mpi, pthreads, and openmp: a performance study. Pattern Recognition in Bioinformatics. Springer, Berlin, pp 424–435
no DOI — not checked{r D e v e l o p m e n t C o r e T e a m} (2010) R: a language and environment for statistical computing
no DOI — not checkedCesarini F, Thompson S (2009) Erlang programming, 1st edn. O’Reilly Media, Inc., Sebastopol, CA
no DOI — not checkedHudak P, Peterson J, Fasel J (2000) A gentle introduction to haskell, version 98.
http://haskell.org/tutorial/
no DOI — not checkedOdersky M, Spoon L, Venners B (2008) Programming in scala. Artima, Walnut Creek CA
no DOI — not checkedBezanson J, Karpinski S, Shah VB, Edelman A (2012) Julia: a fast dynamic language for technical computing. CoRR. abs/1209.5145
no DOI — not checkedAlexandrescu A (2010) The D programming language, 1st edn. Addison-Wesley Professional, Boston, MA. 460p
no DOI — not checkedGriesemer R, Pike R, Thompson K (2009) The Go programming language.
http://golang.org/
no DOI — not checkedWelch P, Aldous J, Foster J (2002) Csp networking for java (jcsp. net). Comput Sci 2002:695–708
no DOI — not checkedSufrin B (2008) Communicating scala objects. Communicating Process Architectures, p 35
no DOI — not checkedStrozzi F, Wurmus R, Roel J et al (2017) Data, workflow example and docker files for scalability and reproducibility chapter.
https://github.com/EvolutionaryGenomics/scalability-reproducibility-chapter
no DOI — not checkedStrozzi F, Wurmus R, Roel J et al (2017) Docker images for scalability and reproducibility chapter.
https://hub.docker.com/u/evolutionarygenomics/
no DOI — not checkedCourtès L (2013) Functional package management with guix. CoRR. abs/1305.4584
no DOI — not checkedAmstutz P, Crusoe MR, Tijanić N et al (2016) Common workflow language, v1.0
no DOI — not checkedStallman R, Mcgrath R (1989) Gnu make: a program for directing recompilation. Free Software Foundation, Boston, MA
no DOI — not checkedKoenig D, Glover A, King P, Laforge G, Skeet J (2007) Groovy in action. Manning Publications Co. Greenwich, CT
no DOI — not checked(2017) Ga4gh platform for docker-based tools and workflows sharing.
https://dockstore.org
no DOI — not checkedAmdahl GM (1967) Validity of the single processor approach to achieving large scale computing capabilities. In: Proceedings of the April 18-20, 1967, Spring Joint Computer Conference. ACM, Washington, DC, pp 483–485
no DOI — not checked(2015) Reproducible builds https://reproducible-builds.org.
https://reproducible-builds.org
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work were clean at the dated check: each resolved to a known work in a public registry, and none
carried a publisher retraction notice at that time. It says nothing about the quality, findings,
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