Five online tools that aim to save researchers time and trouble

From investigating a lab’s publication history to scanning manuscripts for statistical errors, these apps can help streamline some of the most time-consuming tasks.

23 June 2021

Dalmeet Singh Chawla

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An expanding kit of digital tools and apps helps researchers automate certain processes and make others less burdensome.

Nature Index has selected five recently launched or revised tools that aim to make academic life easier, whether you’re thinking of relocating to a new lab, organizing your references or readying a manuscript for submission.

1) Choosing the right lab

Job-hunting can be tough, particularly if interstate or overseas relocation is on the cards. Before you commit to a new position, it’s useful to have some insight into your prospective supervisor, as well as the kind of lab culture you’d be stepping into.

A new tool called Super Researcher aims to make it easier for doctoral and postdoctoral candidates to compare lab leaders based on their productivity and impact.

Described in a bioRxiv paper published in February 2021, the app allows academics to run searches on specific researchers to see their numbers of annual publications, citation counts and details on their most frequent collaborators. The tool pulls publication data from the Scopus database.

The team behind the app, led by co-creator Sheah Lin Lee, a cancer researcher at the University of Southampton in the UK, is working to move it beyond the pilot stage. One challenge, she says, is that it’s hosted on a free (and sometimes unreliable) server, which means it’s prone to the occasional crash – something the team is hoping address in the future.

Lee says she hopes her tool will give researchers a ‘rough and ready’ indication of a lab’s publication culture, which could factor into their decision to take up a new position there. But she urges users to take other factors into consideration, too.

“We don’t think that people should judge whether you want to go to a lab solely based on publications,” says Lee.

2) A spell-checker for statistics

What if there were a way to automatically scan a manuscript for statistical errors while writing your manuscript?

Statcheck, launched in 2015, aims to do so by recalculating p-values — a controversial but commonly used technique to measure statistical significance.

It initially received mixed reactions from academics, but has since gained more acceptance after a preprint study found that it was correct in more than 95% of its recalculations of p-values.

Statcheck has become a popular way to check manuscripts before submission to a journal, says co-creator Michèle Nuijten, who studies analytical methods at Tilburg University in the Netherlands.

It’s also being used by journals such as Psychological Science and the Journal of Experimental Social Psychology to weed out statistical mistakes during the peer-review process.

In 2020, Nuijten and her team expanded the functionality of statcheck by creating a free plugin to be used within Microsoft Word that works like a statistical spell-checker.

Nuijten cautions against using the tool as a means to imply fraud or wrongdoing, emphasizing how easy it can be, even for experienced researchers, to make mistakes in their calculations.

“We all make mistakes. It doesn’t mean we want to,” she says.

3) Spot the difference between preprint versions

Comparing different iterations of a manuscript on preprint servers such as arXiv can be a time-consuming process, says Sharvil Nanavati, a software engineer based in Mountain View, California.

After trying to find a tool to address this, Nanavati and Sergei Taguer, a software engineer in California, decided to build one themselves, which they launched in May 2021.

ArXiv Diff, which was built on top of an existing open-source tool, allows users to view manuscript updates by replacing the word “arxiv” in the URL of a paper to “arxivdiff” then clicking “Show Diff”.

So far, feedback on the new app has been mixed, Nanavati admits. Some academics have praised its usefulness, while others have pointed out that it doesn’t work on all manuscripts.

Nanavati says he’s tweaking the tool’s code to cater for cases where users flag errors. He says the tool, which is a labour of love, will continue to be available for free, but is limited to manuscripts posted to arXiv for now.

4) Find references to papers flagged on PubPeer

It’s becoming increasingly difficult to keep up with the commentary around new papers. Some of these discussions take place on Pubpeer, an online platform where researchers debate the veracity and robustness of specific papers.

While it’s possible to manually check a paper on PubPeer to see if people are talking about it, doing that for an entire reference list can be laborious.

In 2019, PubPeer launched a free plugin on Zotero, an open-source reference-management system that is popular among academics because it hosts a number of plugins with functions such as helping users find free versions of paywalled papers and flagging papers that have been retracted.

The new PubPeer plugin flags any references in a researcher’s paper shortlist — where they save studies that are potentially of interest and may be worthy of citing — that are being discussed on PubPeer, listing the number of comments.

PubPeer also has a browser extension that alerts researchers if they are citing a paper that is being discussed on the platform.

Boris Barbour, co-organizer of PubPeer and a neuroscientist at the Ecole Normale Supérieure’s Institute of Biology in France, says that while there are no immediate plans to expand the new plugin to reference management systems other than Zotero, “there are fairly significant incremental improvements and polishing that could be done”.

5) Scanning for predatory references

In May 2021, Edifix, a bibliographic referencing tool run by Boston-based publishing software firm Inera, expanded its capability to automatically flag references to papers published in predatory journals.

Inera teamed up with Cabell’s International, a scholarly-services firm headquartered in Beaumont, Texas, to access its list of predatory journals, which is usually pay-to-view.

When users check their references using Edifix, in addition to automatically formatting them and fixing any errors, the tool will flag any publications that Cabell’s has identified as predatory. Users can click on those references for an explanation of why the particular journal has been flagged as questionable.

However this new functionality will be free to use for Edifix subscribers until the end of 2021. After that, users will need to pay for a subscription to Cabell’s, says Elizabeth Blake, director of business development at Inera.

The decision to delete or retain references to flagged publications lies with the researcher, says Blake, as it’s possible for subpar journals to publish solid research, and there may be legitimate reasons to cite such work.

Edifix also highlights any references that have been retracted – which a growing number of other bots also do.

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