Editorial: the 18th annual Nucleic Acids Research web server issue 2020.

The 2020 version of Nucleic Acids Research's web server issue marks a change. This 18th web server issue is the first one to be assembled without the editorial supervision of Gary Benson, who served as its executive editor for more than a decade and whose work has made the issue the most prominent resource for scientific web-based applications.

Along with Gary, two of the three website reviewers who helped us to examine and confirm whether web server issue proposals were ‘publication-ready’ stepped back. Thank you, Sean Corbett and David Jenkins, for the excellent work you did for the web server issue. I should not forget to thank Gary's wife, Fay Oppenheim, who helped him (and myself over the last year) by keeping all the proposals, authors and reviewers organized. It is hard to imagine how the web server issue would have been possible without her constant support.

And, last but not least, thank you Gary for inviting me as your successor. You left very large footprints and I will try my best to fill them.

Without Fay's help, the well-rehearsed historical system of sending proposals by email became impossible—she used to extract all the essentials such as author names, URLs, etc. from the mails, PDFs or Word documents and entered them into a database. All readers who have tried to write algorithms capable of reliably retrieving author data from unformatted text will know that this is not possible without curation, so I decided to set-up an upload portal for proposals instead (https://nar.bihealth.de/).

As in the past, proposals were first editorially checked for their suitability and afterwards, websites or stand-alone tools were tested before allowing the submission of a manuscript. Together with Martine Bernardes-Silva, NAR’s editorial manager, we decided to use Scholar One's system of manuscript invitations for the successful proposals. With this infrastructure, handling the 274 proposals we received this year became feasible.

One of the past website reviewers, Adam Simpkin, is still on board and I found three other reviewers. These are our current website examiners:

Adam Simpkin holds a PhD in X-ray crystallography and is at the University of Liverpool, UK.

Piotr Grabowski owns a PhD in computational systems biology and works for AstraZeneca in Cambridge, UK.

Lennard Ostendorf is a medical doctor and a PhD student at the Charité – Universitätsmedizin Berlin, Germany.

Sebastian Proft is a bioinformatician and PhD student in my group at the Berliner Institut für Gesundheitsforschung (Berlin Institute of Health), Germany.

Of course, the change of the team and the move to a new infrastructure caused some teething pains, so the proposal and website reviews took longer than before. I apologize for the delay and promise faster decisions for the next issue.

The biggest challenge for all of us was, however, the Covid-19 pandemic. My group's offices have been turned into a temporary intensive care unit and most labs were closed. Many reviewers were hence not able to deliver their reports in time and many authors had difficulties submitting their revisions. Nevertheless, we managed to finish this year's Issue in time, and I want to use the opportunity to thank everyone for their work despite the crisis.

However, closed labs, lost offices, or delayed publications are certainly a small sacrifice compared to the many people who lost their lives, family members or friends, their jobs or those who could not meet their loved ones for a long time.

This year's web server issue contains the following manuscripts:

We received 273 proposals for this year's Web Server Issue, including four duplicates. Of these 269 proposals, exactly 100 (37%) were allowed to submit a manuscript. One manuscript was never submitted and another one retracted. Seventy nine manuscripts were finally accepted after peer-review (29% acceptance rate of proposals, 81% acceptance rate of submitted manuscripts).

The main reasons for an early rejection of manuscripts were:

Proposal of a new method or focus on a single dataset

The web server issue is not aimed at publishing new approaches, its primary role is to collect user-friendly (mainly web-based) interfaces for established tools or methods. Many of the proposals rejected either proposed new methods (such as machine learning-based classifiers) and/or were aimed at analysis/visualization of a single dataset, which is mainly relevant for the authors themselves.

Lack of user-friendliness/lacking or insufficient documentation

Software published in the web server issue must be easy-to-use, and well-documented. We will not accept manuscripts if software or documentation do not fulfill these criteria.

No benefit over existing approaches

Tools such as R Shiny make it easy for non-programmers to produce web-based applications. While we have published web servers based on Shiny in the past and will continue to do so, these must provide a significant benefit over using the underlying R package without a web server, e.g. by providing an easy-to-use input, a user-friendly output, and extended visualization options. If users retrieve results only as R data frames and must hence use R anyway to handle them, there is no advantage in having a web server.

With the advent of web servers able to handle complete exomes or even genomes of humans, there is another problem emerging: data security and privacy.

One reviewer who studied a web server in more detail than we did, found a relatively simple way to access data uploaded by other users. We are very grateful to you! This was of course a wake-up call for us to put more emphasis on security/privacy issues when testing websites. But it also questioned our previous policy of forbidding logins—these are of course safer than URLs including a private accession ID. This point was indeed raised by several referees and we have thus decided to allow logins if—and only if—personal data such as human WGS or WES data is transmitted. For such websites, we will also require SSL (https) encryption. To ensure free access, users must be able to obtain a login without a working email address.

In the first paragraph I wrote that, thanks to Gary Benson's work, the NAR web server issue has become the most prominent resource for scientific web servers. This is illustrated in an unpublished study by Andreas Keller's group from Universität des Saarlandes, Saarbrücken, Germany. They extracted articles describing web services of all kind from PubMed and checked whether the services are still available. As shown in Figure 1A, NAR has published more web servers than any other journal in the last ten years and a high proportion of these are still running (Figure 1B). We are of course very proud of these numbers—thank you for sharing them. I hope that your study will resolve in a web-based database that will show which authors keep their web servers alive after publication.

Figure 1.

(A) Web services published since 2010, (B) Percentage of available web services published after 2015.

With this encouraging study, I will close my first editorial. In addition to those mentioned above, I want to thank the other editors of NAR and the staff at Oxford University Press for their support, especially our publisher, Joanna Ventikos.

But most of all I am grateful to the authors and reviewers who did a remarkable job in these difficult times.

Please check https://academic.oup.com/nar/pages/submission_webserver for any changes of deadline or requirements by November if you want to submit to the 2021 web server issue.

Short title	URL	Short description
TeamTat	https://www.teamtat.org	Collaborative text annotation
SIBiLS	http://candy.hesge.ch/SIBiLS	RESTful customizable search engine for biomedical literature
PDBMD2CD	https://pdbmd2cd.cryst.bbk.ac.uk/	Prediction of protein circular dichroism spectra
AWSEM-Suite	https://awsem.rice.edu/	Protein structure prediction based on coevolution and coarse-grained force field
TopMatch-web	https://topmatch.services.came.sbg.ac.at	3D matching of large assemblies of protein and nucleic acid chains
ShiftCrypt	http://bio2byte.be/shiftcrypt/	Biophysical alignment of proteins through NMR chemical shift values
ARIAweb	https://ariaweb.pasteur.fr	Automated NMR protein structure calculation
ProteinsPlus	https://proteins.plus	Interactive analysis of protein–ligand binding interfaces
HomolWat	http://lmc.uab.cat/homolwat/	Incorporation of ‘homologous’ water molecules into G protein-coupled receptor structures
FATCAT 2.0	http://fatcat.godziklab.org/	Comparison of the structural diversity of proteins
Zebra2	https://biokinet.belozersky.msu.ru/zebra2	Analysis of subfamily-specific and conserved positions in protein superfamilies
TREND	http://trend.zhulinlab.org/	Exploring protein function in prokaryotes
PlaToLoCo	http://platoloco.aei.polsl.pl/	Annotation of low complexity regions in proteins
piNET	http://pinet-server.org	Analysis and visualization of proteomics data
WebPSN	http://webpsn.hpc.unimore.it	Inference fingerprints of structural communication in biomacromolecules
EnzymeMiner	http://loschmidt.chemi.muni.cz/enzymeminer	Automated selection of putative enzymes
Conserved Unique Peptide Patterns (CUPP)	https://www.cupp.info	Functional annotation of carbohydrate active enzymes
AlloSigMA 2	http://allosigma.bii.a-star.edu.sg	Designing allosteric effectors and using allosteric effects of variants
mmCSM-AB	http://biosig.unimelb.edu.au/mmcsm_ab/	Guiding rational antibody engineering through multiple point mutations
MISCAST	http://miscast.broadinstitute.org/	Visualization and analysis of missense variants in protein sequences
MusiteDeep	https://www.musite.net	Post-translational modification site prediction and visualization
mCSM-membrane	http://biosig.unimelb.edu.au/mcsm_membrane/	Predicting the effects of variants on transmembrane proteins
LIST-S2	https://list-s2.msl.ubc.ca/	Prioritization of deleterious missense mutations in different species
VarFish	https://varfish-kiosk.bihealth.org	Collaborative exome analysis for clinic and research
3D-GNOME	http://3dgnome.cent.uw.edu.pl/	predicting structural variation-driven alterations of chromatin spatial structure in the human genome
Galaxy HiCExplorer	https://hicexplorer.usegalaxy.eu	Promoter capture Hi-C and single-cell Hi-C data analysis, quality control and visualization
SNPnexus—2020 update	https://www.snp-nexus.org/	Functional annotation of human genome sequence variation
EpiRegio	https://epiregio.de	Analysis and retrieval of regulatory elements linked to genes
InteractomeSeq	https://interactomeseq.ba.itb.cnr.it/	Identification and profiling of domains and epitopes from Phage Display and Next Generation Sequencing data
TFmotifView	http://bardet.u-strasbg.fr/tfmotifview/	Visualization of transcription factor motifs in genomic regions
RiboToolkit	http://rnabioinfor.tch.harvard.edu/RiboToolkit	Decoding RNA translation
AnnoLnc	http://annolnc.gao-lab.org	Annotation of novel lncRNAs in human and mouse
mRNALoc	http://proteininformatics.org/mkumar/mrnaloc	Predicting mRNA subcellular localisation
miRNet 2.0	https://www.mirnet.ca/	miRNA functional analysis
miRViz	http://mirviz.prabi.fr/	Visualization and interpretation of microRNA datasets
mirnaQC	https://arn.ugr.es/mirnaqc/	Comparative quality control of miRNA-seq data
miRSwitch	https://anathema.cs.uni-saarland.de/mirswitch/	miRNA arm switch event finder
IRIS3	https://bmbl.bmi.osumc.edu/iris3/	Inference of cell-type-specific regulons from single-cell RNA-seq
MutaRNA	http://rna.informatik.uni-freiburg.de/MutaRNA	Analysis and visualization of mutation-induced changes in RNA structure
RNAProbe	https://iimcb.genesilico.pl/shape/	Normalization and analysis of RNA structure probing data
rMAPS2	http://rmaps.cecsresearch.org/	RNA map analysis for alternative splicing regulation
SPEED2	https://speed2.sys-bio.net/	Inferring upstream pathway activity from differential gene expression
FGviewer	https://ccsmweb.uth.edu/FGviewer	Visualization of functional features of human fusion genes
PseudoChecker	http://pseudochecker.ciimar.up.pt/	Automated discovery of pseudogenes
OligoMinerApp	http://oligominerapp.ingm.org/	Design of genome-scale oligonucleotide in situ hybridization probes
BE-FF	http://danioffenlab.pythonanywhere.com/BE-FF	Prediction of synonymous corrections for CRISPR/Cas
PaCRISPR	http://pacrispr.erc.monash.edu/	prediction of anti-CRISPR proteins
AcrFinder	http://bcb.unl.edu/AcrFinder	Search for anti-CRISPR operons in prokaryotes and their viruses
NanoSPC	https://nanospc.mmmoxford.uk/	A nanopore metagenomic data processing pipeline
CReSCENT	http://crescent.cloud	Cancer single-cell transcriptomics data analysis
The Omics Discovery REST interface	https://www.omicsdi.org/ws/	Access, discovery and dissemination of omics datasets
BIOMEX	https://www.vibcancer.be/software-tools/biomex	Single cell omics data interpretation and visualization
Galaxy Collections	http://galaxyproject.org	2020 update of the Galaxy platform for collaborative biomedical analyses
ASAP	https://asap-beta.epfl.ch/	Single-cell omics analyses
Oviz-Bio	https://bio.oviz.org	Interactive cancer genomics data visualization
Fluxer	https://fluxer.umbc.edu	Computation and analysis of genome-scale metabolic flux networks
NOREVA 2.0	https://idrblab.org/noreva2020/	Normalization and evaluation of time-course and multi-class metabolomic data
NetMHCpan-4.1 and NetMHCIIpan-4.0	http://www.cbs.dtu.dk/services/NetMHCIIpan-4.0/	Predictions of MHC antigen presentation
ToxicoDB	http://toxicodb.ca/	Mining large-scale toxicogenomic datasets
CVCDAP	http://omics.bjcancer.org/cvcdap/	Platform for molecular and clinical analysis of cancer virtual cohorts
Tox21BodyMap	https://sandbox.ntp.niehs.nih.gov/bodymap/	Mapping chemical effects on the human body
novoPathFinder	http://design.rxnfinder.org/novopathfinder/	Designing novel pathways
SynergyFinder 2.0	https://synergyfinder.fimm.fi	Visual analytics of multi-drug combination synergies
SYNERGxDB	http://SYNERGxDB.ca/	Identification of synergistic drug combinations for precision oncology
PaccMann	https://ibm.biz/paccmann-aas	Explainable anticancer drug sensitivity prediction
TIMER2.0	http://timer.cistrome.org/	Analysis of tumor-infiltrating immune cells
GeneTrail 3	http://genetrail.bioinf.uni-sb.de	High-throughput enrichment analysis
miEAA 2.0	https://ccb-compute2.cs.uni-saarland.de/mieaa2	Gene-set enrichment including multi-species microRNA analysis
LINbase	http://linbase.org	Genome-based identification of prokaryotes
The Quest for Orthologs Continuous Benchmark Service and Consensus Calls 2020	https://orthology.benchmarkservice.org/	Benchmarking the identification of orthologs
ARTS 2.0	http://arts.ziemertlab.com	Antibiotic Resistant Target Seeker for comparative genome mining
MetaPhOrs	http://orthology.phylomedb.org/	Phylogeny-based inference of orthology and paralogy
COVTree	http://www.lcqb.upmc.fr/COVTree/	study co-evolution in overlapped sequences
CoCoCoNet	http://milton.cshl.edu/CoCoCoNet	Co-expression in different species
MetaNets	https://web.rniapps.net/metanets/	Inference of microbial correlation networks
SuperCypPred	http://insilico-cyp.charite.de/SuperCYPsPred/	Prediction of cytochrome activity
InterPred	https://sandbox.ntp.niehs.nih.gov/interferences/	Prediction of chemical autofluorescence and luminescence interference
Atomic Charge Calculator II	http://ncbr.muni.cz/ACC2	Calculation of partial atomic charges
CausalMGM	http://causalmgm.org	A causal discovery tool