The Front Matter Blog covers the intersection of science and technology since 2007.

This Monday ORCID, CrossRef and DataCite announced (ORCID post, CrossRef post, DataCite post) the new auto-update service that automatically pushes metadata to ORCID when an ORCID identifier is found in newly registered DOI names. This is the first joint announcement by the three organizations, and shows the close collaboration between ORCID, CrossRef and DataCite.

DataCite

Explaining the DataCite/ORCID Auto-update

In this post I want to talk about some of the misunderstandings I frequently encounter when discussing markdown as a format for authoring scholarly documents. Scholars will always use Microsoft Word Microsoft Word is of course what almost all authors use in the life sciences and many other disciplines. One big reason for this is the file formats accepted my manuscript submission systems.

Public Library of Science

In this post I want to talk about some of the misunderstandings I frequently encounter when discussing markdown as a format for authoring scholarly documents.Scholars will always use Microsoft Word  Microsoft Word is of course what almost all authors use in the life sciences and many other disciplines. One big reason for this is the file formats accepted my manuscript submission systems.

Six Misunderstandings about Scholarly Markdown

Yesterday PLOS Biology published an essay by me: What Can Article Level Metrics Do for You? (Fenner, 2013). I had help from many others in writing the essay, in particular PLOS Biology editor Emma Ganley. I hope that the essay can help researchers get introduced to article-level metrics, and I am honored that the essay is part of the PLOS Biology 10th anniversary collection.

What Can Article-Level Metrics Do for You?

Inspired by four recent blog posts and their comments (Comments at journal websites: just turn them off, Open Access and The Dramatic Growth of PLoS ONE, No Comment?, If you email it, they will comment), I created a graphic to show what users do with PLoS ONE papers. As always, the data behind the graphic are openly available.

What Users do with PLOS ONE Papers

In July Wiley published the book Visualize This – The Flowing Data Guide to Design, Visualization and Statistics. The book is written by Nathan Yau, and he is of course also behind the popular FlowingData blog about the same topic. This is a short review of the book. Please keep in mind that I’m no expert in data visualization. The book is written for people like me, an expert in the topic will probably look at the book differently.

Medizinische Hochschule Hannover

In July Wiley published the book

 
 Visualize This – The Flowing Data Guide to Design, Visualization and Statistics
 

. The book is written by

 
 Nathan Yau
 

, and he is of course also behind the popular FlowingData blog about the same topic. This is a short review of the book. Please keep in mind that I’m no expert in data visualization.

Book Review: Visualize This by Nathan Yau

The reference management software Papers has been a regular topic on this blog.

Papers 2: the reference manager made with love

One of the annoyances with bibliographies as we use them for scholarly papers is that is usually unclear why a particular paper was cited. It is often possible for readers to gather this information by looking at the citation in the context of the surrounding text, but this is very difficult to automate.

How to use Citation Typing Ontology (CiTO) in your blog posts

Lanyrd is a new social directory for conferences launched just a few days ago. It integrates with Twitter to allow you to list conferences you are organizing, speaking at, attending, or just following. It is a social directory in the sense that everyone can edit this information (I don’t know who started the Science Online London 2010 page), and that you can see the conferences of your Twitter contacts.

Lanyrd: a new Twitter mashup for conferences

Last week I received email invitations from three different journals to submit a research article. I should have felt flattered, but it is unclear why it is me that received invitations to the journals Biomarker Insights, Genomics Insights and International Journal of Medical Sciences. All three journals already exist for a few years, and I wouldn't say that the focus of my research is biomarkers or genomics.

Last week I received email invitations from three different journals to submit a research article. I should have felt flattered, but it is unclear why it is me that received invitations to the journals

 Biomarker Insights

,

 Genomics Insights

and

 International Journal of Medical Sciences

. All three journals already exist for a few years, and I wouldn't say that the focus of my research is biomarkers or genomics.

When calls for papers go wrong

Picking the right journal is one of the most important decisions when you start to work on a paper. You probably have a gut feeling of the journals that are best suited for your paper in progress. To make this decision more objective, you can rely on the Impact Factor of a journal. The Impact Factor is roughly the average number of citations per paper in a given journal and is published by  Thomson Scientic.

Tired of Impact Factors? Try the SJR indicator

The Howard Hughes Medical Institute (HHMI) today announced that it will support Open Access in Springer journals through the Springer Open Choice program.

Howard Hughes Medical Institute pays for Open Access in Springer journals

This is the November issue of the monthly newsletter from the Rogue Scholar science blog archive. The newsletter reports on new blogs that have joined the platform, important technical updates in Rogue Scholar infrastructure, community updates, and other news relevant to Rogue Scholar users. Blogs added to Rogue Scholar Two blogs were added in November. Welcome!

Front Matter

This is the November issue of the monthly newsletter from the Rogue Scholar science blog archive. The newsletter reports on new blogs that have joined the platform, important technical updates in Rogue Scholar infrastructure, community updates, and other news relevant to Rogue Scholar users.Blogs added to Rogue Scholar  Two blogs were added in November. Welcome!

Rogue Scholar Newsletter November 2025

This is the December 2025 issue of the monthly newsletter from the Rogue Scholar science blog archive. The newsletter reports on new blogs that have joined the platform, important technical updates in Rogue Scholar infrastructure, community updates, and other news relevant to Rogue Scholar users.

This is the December 2025 issue of the monthly newsletter from the Rogue Scholar science blog archive. The newsletter reports on new blogs that have joined the platform, important technical updates in Rogue Scholar infrastructure, community updates, and other news relevant to Rogue Scholar users.Blogs added to Rogue Scholar  Three blogs were added in November. Welcome!

Rogue Scholar Newsletter December 2025

This is the September issue of the monthly newsletter from the Rogue Scholar science blog archive. The newsletter reports on new blogs that have joined the platform, important technical updates in Rogue Scholar infrastructure, community updates, and other news relevant to Rogue Scholar users. Blogs added to Rogue Scholar One blog was added in September. Welcome!

This is the September issue of the monthly newsletter from the Rogue Scholar science blog archive. The newsletter reports on new blogs that have joined the platform, important technical updates in Rogue Scholar infrastructure, community updates, and other news relevant to Rogue Scholar users.Blogs added to Rogue Scholar  One blog was added in September. Welcome!

Rogue Scholar Newsletter September 2025

Personal names remain among the hardest scholarly metadata to capture properly, including for science blog posts. This week, the Rogue Scholar science blog archive therefore changed how it stores blog post author names: no longer as name, which is the standard in RSS, Atom, and JSON Feeds, but as name only for an organizational author, and as given and family name for personal authors.

Personal names remain among the hardest scholarly metadata to capture properly, including for science blog posts.

Personal names in science blogs

From October 21 to 27 is International Open Access Week 2024, and this blog post summarizes my contribution for 2024. Open Access Week 2024 will continue the call to put “Community over Commercialization” and prioritize approaches to open scholarship that serve the best interests of the public and the academic community.

From October 21 to 27 is International Open Access Week 2024, and this blog post summarizes my contribution for 2024. The title of this post was taken from a blog post by my friend and colleague Heinz Pampel on Monday, and we again have many events related to International Open Access Week this week, as well as some blog posts. This brings me to Rogue Scholar, the science blog archive I launched in 2023 which is the main focus of my work.

My contribution to Open Access Week 2024

The Rogue Scholar science blog archive is built with Open Source software, starting with Javascript in June 2023 and adding an API written in Python in October 2023. This week I am releasing the first version of commonmeta written in Go to simplify the Rogue Scholar backend.

Rogue Scholar is learning a new language

From the start last year one important goal for the Rogue Scholar science blog archive was to make it easy to use for blog authors and readers. Today I want to focus on another aspect: keep it simple to run Rogue Scholar infrastructure. To address that goal I started development work last week to further simplify one important aspect of Rogue Scholar infrastructure: metadata conversion.

Simplifying Rogue Scholar Infrastructure

Today the Rogue Scholar science blog archive launched a new feature: Rogue Scholar Preview. This new functionality enables the import of new science blogs into the preview version of the production service, located at https://preview.rogue-scholar.org. This allows users to see how their blog posts will look like in the Rogue Scholar service, and to resolve issues if necessary.

Today the Rogue Scholar science blog archive launched a new feature:

 Rogue Scholar Preview

. This new functionality enables the import of new science blogs into the preview version of the production service, located at https://preview.rogue-scholar.org. This allows users to see how their blog posts will look like in the Rogue Scholar service, and to resolve issues if necessary.

Announcing Rogue Scholar Preview

The science blog archive that I have started to work on (see previous posts) finally has a name: the Rogue Scholar. I picked this name because I liked the description in the Urban Dictionary. A person with extensive knowledge pertaining to various subject matters that extends beyond formal education. This person often gathers knowledge from various sources, such as media, friends, casual reading or the internet.

The science blog archive that I have started to work on (see previous posts) finally has a name: the

 Rogue Scholar

. I picked this name because I liked the description in the Urban Dictionary.

Sign up for the science blog archive waitlist

In October Jen Gibson started as the new Executive Director for the Dryad Data Repository. I used the opportunity to ask Jen a few questions about Dryad, challenges with data sharing, and ideas about moving Dryad forward. I was particularly interested in the interview as I served on the Dryad Board of Directors from 2013 to 2016.

Dryad: Interview with Jen Gibson

DataCite is a DOI registration agency that enables the registration of scholarly content with a persistent identifier (DOI) and metadata. This content can then be searched for, reused, and connected to other scholarly resources. But how does the underlying infrastructure enable this? In this blog post, we will describe what we have built to make this work. This is a fairly technical post, as I tried to go a little deeper into the details.

The DataCite Technology Stack

Persistent identifiers (PIDs) are not only important to uniquely identify a publication, dataset, or person, but the metadata for these persistent identifiers can provide unambiguous linking between persistent identifiers of the same type, e.g. journal articles citing other journal articles, or of different types, e.g. linking a researcher and the datasets they produced.

Introducing the PID Graph

Today we are announcing our first new functionality of 2019, a much improved search for DataCite DOIs and metadata. While the DataCite Search user interface has not changed, changes under the hood bring many important improvements and are our biggest changes to search since 2012. Faster Indexing Newly registered (and tagged findable) DOIs now appear in the DataCite Search index within a few minutes, compared with the previous up to 12 hour lag.

Today we are announcing our first new functionality of 2019, a much improved search for DataCite DOIs and metadata. While the DataCite Search user interface has not changed, changes under the hood bring many important improvements and are our biggest changes to search since 2012.Faster Indexing  Newly registered (and tagged findable) DOIs now appear in the DataCite Search index within a few minutes, compared with the previous up to 12 hour lag.

DataCite's New Search

Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for the scholarly outputs we produce.

Eating your own Dog Food

CSV in many ways is for data what Markdown is for text documents: a very simple format that is both human- and machine-readable, and that – despite a number of shortcomings - is widely used. Given the popularity of Markdown for writing blog posts, using CSV to publish blog posts with tabular data should be an obvious thing to do, and we have just published our first blog post using CSV data.

Publishing tabular data as blog post

Last week Jennifer Lin shared information on the Making Data Count (MDC) project on this blog. MDC is a project funded by the U.S. National Science Foundation (NSF) to design and develop metrics that track and measure data use – data-level metrics (DLM). Funding for the 12 month project ends October 1st, with a no-cost extension until March 1st. MDC is a research project and has delivered some interesting questions and important results.

Last week Jennifer Lin shared information on the

 Making Data Count

(MDC) project on this blog. MDC is a project funded by the U.S. National Science Foundation (NSF) to design and develop metrics that track and measure data use –

 data-level metrics

(DLM). Funding for the 12 month project ends October 1st, with a no-cost extension until March 1st.

Announcing Data-Level Metrics in DataCite Labs

Today DataCite received an email from a user alerting us that there are some small inconsistencies with our recommended data citation format: Creator (PublicationYear): Title. Publisher. Identifier at https://www.datacite.org/services/cite-your-data.html Creator; (PublicationYear): Title; Publisher.

Today DataCite received an email from a user alerting us that there are some small inconsistencies with our recommended data citation format:Creator (PublicationYear): Title. Publisher. Identifier at https://www.datacite.org/services/cite-your-data.htmlCreator; (PublicationYear): Title; Publisher.

Overcoming Development Pain

The iTunes Store was opened by Apple in 2003 to sell digital music and other digital assets. Since 2009 music purchased in the iTunes store is free of Digital Rights Management (DRM). Apple became the largest music vendor worldwide in 2010, and by 2013 had sold 25 billion songs. Scholarly articles are distributed almost exclusively in digital form.

Why there is no iTunes for science papers

Opening Science: The Evolving Guide on How the Internet is Changing Research, Collaboration and Scholarly Publishing is a SpringerOpen book (using a Creative Commons Attribution-NonCommercial license) that will be published in a few weeks. If you can’t wait for the book to be published and/or you want to make comments or suggestions, go to the dynamic book online version at http://book.openingscience.org.

Opening Science - the Book

Article-level metrics (ALMs) provide a wide range of metrics about the uptake of an individual journal article by the scientific community after publication. They include citations, usage statistics, discussions in online comments and social media, social bookmarking, and recommendations.

Article-level metrics (ALMs) provide a wide range of metrics about the uptake of an individual journal article by the scientific community after publication. They include citations, usage statistics, discussions in online comments and social media, social bookmarking, and recommendations.

Authoring of scholarly articles is a recurring theme in this blog since it started in 2008. Authoring is still in desperate need for improvement, and nobody has convincingly figured out how to solve this problem. Authoring involves several steps, and it helps to think about them separately:  * Writing. Manuscript writing, including formatting, collaborative authoring  * Submission.

Authoring of scholarly articles is a recurring theme in this blog since it started in 2008. Authoring is still in desperate need for improvement, and nobody has convincingly figured out how to solve this problem. Authoring involves several steps, and it helps to think about them separately:

 
 Writing
 

. Manuscript writing, including formatting, collaborative authoring

 
 Submission
 

.

The Grammar of Scholarly Communication

This Friday and Saturday the SpotOn London Conference will take place at the British Library in London. I am very excited, as I have come to this conference since the first one in 2008, and have helped organize the event since 2009. The conference is about science communication in the broadest sense, and has three strands that focus on science communication, science policy and tools.

This Friday and Saturday the SpotOn London Conference will take place at the British Library in London. I am very excited, as I have come to this conference since the first one in 2008, and have helped organize the event since 2009.

What is the Value of Hack Days?

On Saturday, June 8th – exactly a month from today – the PLOS San Francisco offices will host a workshop/hackathon about using markdown for science. A lot of people are experimenting with markdown for authoring scientific articles – see blog posts here, here or my post here, and the scientific manuscript here.

Announcing Markdown for Science Workshop on June 8th

Today the journal Nature has released a special on the Future of Publishing. It includes a lot of interesting reading, but I want to focus on the comment Beyond the Paper by Jason Priem.

Today the journal

 Nature

has released a special on the Future of Publishing. It includes a lot of interesting reading, but I want to focus on the comment Beyond the Paper by Jason Priem.

Some Thoughts on Beyond the Paper

Last week I attended the altmetrics12 workshop in Chicago. You can read all 11 abstracts here, and the conference had good Twitter coverage (using the hashtag #altmetrics12), at least until Twitter had a total blackout around 12 PM our time. All but two presenters used slides – I have uploaded my presentation to Speaker Deck.

Random notes from the altmetrics12 conference

This was another week with a fair amount of spam in my email inbox. We all receive email spam on a regular basis and most of us have probably also received science spam: invitations to scientific conferences about topics we are not working on, invitations to submit articles to journals not covering your field, and information about lab supplies we never had asked for.

A Few Questions about Science Spam

Zotero 3.0 was officially released today. The big change in version 3.0 of the reference manager is a standalone version that runs outside the Firefox browser. The first beta was released in August 2011.

Zotero 3.0 Released

Brendan Thomas has published an interesting paper that looks at author email addresses in the PubMed database of biomedical literature. Email addresses of first authors have been added to PubMed since 1996, and they can be retrieved via the standard web interface or automated software. This makes PubMed an excellent place to find the email address of an academic author, but also shows that PubMed is very vulnerable to email address harvesting.

Did you receive spam because you published a paper?

It’s very unusual for me to post two blog posts in a single day, and even more so when both posts are based on press releases by the same organization. But this is important news for everybody interested in scholarly publishing.

New journal “Nature ONE” launched today

Citations are a fundamental concept of scholarly works. Unfortunately they are also difficult to do. Traditional writing tools such as Microsoft Word can’t really handle them in a way that is appropriate for a scientific manuscript, and that is why we have reference managers such as Endnote, Zotero or Mendeley.

Citations are links, so where is the problem?

Starting this week, the Rogue Scholar science blog archive has consolidated authentication into a single Identity and Access Management (IAM) service, powered by a self-hosted Keycloak instance at https://auth.front-matter.de.

Starting this week, the Rogue Scholar science blog archive has consolidated authentication into a single Identity and Access Management (IAM) service, powered by a self-hosted Keycloak instance at https://auth.front-matter.de. The goal of this consolidation into a single service was to make it easier to enforce three basic rules:Authenticated users must have an ORCID identifier,Authenticated users must have a validated email address,Rogue

Consolidating Rogue Scholar Authentication

Cellular Therapy and Transplantation
 

today published my paper Reference Management meets Web 2.0. Regular readers of this blog probably know about most of the things I talk about in the paper, but I hope it is a good introduction for those new to reference management.

Paper published: Reference Management meets Web 2.0

Last Tuesday the

 
 German Research Foundation
 

(DFG) announced changes to the grant application process, going in effect in July. Researchers are no longer allowed to list all their publications in their grant proposals.

German Research Foundation says that numbers aren’t everything

Just four weeks ago I wrote a blog post titled How do you read papers? 2010 will be different. Not only have we since seen the announcement of the Apple iPad, but last Monday the free Nature.com iPhone app was launched.

Nature.com iPhone app in pictures

Last week the

 New England Journal of Medicine

(

 NEJM

) published a paper on selective outcome reporting in clinical trials (Vedula et al. 2009). The primary and secondary outcome(s) of a clinical trial could for example be survival in cancer patients or rate of heart attacks and other cardiovascular events in patients taking cholesterol-lowering drugs.

Publication bias in clinical trials

The Rogue Scholar archive of scholarly blogs has grown to 34 blogs with about 420 blog posts. In order to implement DOI registration for these blog posts, I needed two things:  * Content and metadata, ideally without requiring blogs to implement anything special.

The Rogue Scholar archive of scholarly blogs has grown to 34 blogs with about 420 blog posts.

Starting to register DOIs for all blog posts included in the Rogue Scholar

Last year

 
 Elsevier
 

started the Article 2.0 Contest and asked for the best ideas on how research articles should be presented on the web.

How does the article of the future look like?

Finishing an exciting research project and writing it up in a paper are the first two steps in getting your work published. The next two steps – submitting your paper to a journal and getting it through the review process – have changed dramatically in the last 10-15 years.

Lemon8-XML: Interview with MJ Suhonos

A recent Nature News article by Geoff Brumfiel (Science journalism: Supplanting the old media?) has stirred up many interesting discussions about the relationship of science blogging and traditional science journalism. Good starting places to follow these discussions (and engage in them) are Technorati, Nature.com Blogs and FriendFeed. Science blogging extends, but also threatens traditional science journalism.

A recent

 Nature News

article by Geoff Brumfiel (Science journalism: Supplanting the old media?) has stirred up many interesting discussions about the relationship of science blogging and traditional science journalism. Good starting places to follow these discussions (and engage in them) are Technorati, Nature.com Blogs and FriendFeed. Science blogging extends, but also threatens traditional science journalism.

Twitter for Peer Review

Today is Open Access Day1, intended to broaden awareness and understanding of Open Access. Many science bloggers have written about Open Access today,and links to a lot of these blog posts have been collected by Bora Zivkovic2 or are found in the FriendFeed room set up for the day3.

Today is Open Access Day

 1

, intended to broaden awareness and understanding of Open Access.

Open Access – what’s in it for me?

The just finished conference Science Blogging 2008: London was a wonderful chance for real-life socialising networking. I started to upload some fotos to Flickr (e.g. Scott Keir explaining sign language, see all fotos tagged sciblog here), some of them are too embarrassing and I will keep them for bribes reference later on. The meeting was also a great opportunity to think about where we are today with scienceblogging.

The just finished conference Science Blogging 2008: London was a wonderful chance for real-life socialising networking. I started to upload some fotos to Flickr (e.g. Scott Keir explaining sign language, see all fotos tagged

 
 sciblog
 

here), some of them are too embarrassing and I will keep them for bribes reference later on. The meeting was also a great opportunity to think about where we are today with scienceblogging.

Science blogging is the new email

Most scientific papers are now published in English, and I believe that this trend is good for international collaboration. Therefore I believe that blogs intended for scientists should also be written in English.

Science Blogging in German

As I said before on this blog, I do like poster sessions. The poster sessions at the just finished American Society of Clinical Oncology meeting didn't offer food and drink, but were otherwise very enjoyable. The meeting is probably special because a lot of high quality research will be presented as poster, as there is just not enough time for enough oral sessions. Many of the poster presenters were senior faculty.

I like poster sessions

In the last issue of Nature, a news feature and research highlight look at two recent high-profile paper retractions. The two papers by biochemist Homme Hellinga delt with rational enzyme design. A second group couldn't reproduce the results, ultimately leading to the paper retractions. Then a third group was able to demonstrate that rational enzyme design is indeed possible.

Designer debacles and other misdemeanors

David Crotty, the Executive Editor from CSH Protocols, last month wrote a provocative blog post called Why Web 2.0 is failing in Biology. He did an informal poll among scientists and found that none of them read science blogs or use social networking sites for scientists. His arguments why that is so?  * Time. Scientists have little time, and rather spend this time in the laboratory or reading papers  * Trust.

David Crotty, the Executive Editor from CSH Protocols, last month wrote a provocative blog post called Why Web 2.0 is failing in Biology. He did an informal poll among scientists and found that none of them read science blogs or use social networking sites for scientists.

Is Web 2.0 failing in Biology?

A Nature News article last week talked about the confusion that happens if a number of authors have the same or similar names (Scientific publishing: Identity crisis). This is apparently a special issue in China because of the difficulties transliterating Chinese characters into English and the use of only a limited number of surnames.

Are names important?

Donald Kennedy, the edior-in-chief of Science, yesterday wrote an editorial about a legal dispute between the New England Journal of Medicine and the drug company Pfizer. Pfizer wants the NEJM to provide the reviewer comments on submitted papers about the two Pfizer products celecoxib (Celebrex) and valdecoxib (Bextra). Both drugs are used to treat pain and belong to the COX-2 inhibitor class of drugs.

Should Peer Review be confidential?

Just Science is an effort to collect blog posts about science that are written within one week. Just Science 2008 will start tomorrow and ends February 8. Science bloggers that agree to participate should write one daily blog entry for these five days.

Just Science starts tomorrow

The Deutsche Ärzteblatt is the official journal of the German Medical Association, just as the British Medical Journal (BMJ) and the Journal of the American Medical Association (JAMA). Starting January 21, an English language version of the journal will be available. The publisher and editors of the journal decided to make this step to have the journal articles better indexed in databases such as PubMed and available to more readers.

Should all papers be published in English?

Buzzword is a free online word processor based on the Adobe Flash technology. I previously wrote about Buzzword and how it could be used to write a scientific paper. The first impressions were positive, so I decided to write my next paper with Buzzword. This paper has been submitted this week. What did I like and dislike about Buzzword? Good Most importantly, there is only one version of your manuscript.

Buzzword is a free online word processor based on the Adobe Flash technology. I previously wrote about Buzzword and how it could be used to write a scientific paper. The first impressions were positive, so I decided to write my next paper with Buzzword. This paper has been submitted this week. What did I like and dislike about Buzzword?Good  Most importantly, there is only one version of your manuscript.

Writing a paper with Buzzword

Kathy Redmond wrote an editorial in the November issue of Nature Clinical Practice Oncology about the media coverage of cancer. She argues that this coverage is frequently of poor quality, reinforcing the myth of cancer as an automatic death sentence and the overemphasis on stories about wonder cures.

Poor media coverage of cancer research: are blogs one answer?

OncologySTAT is a new (it launched September 7) web portal by Reed Elsevier that offers, among many other things, full access to journal articles in Elsevier oncology journals. Elsevier hopes to generate enough revenue from selling advertising on the web site to compensate for (potentially) lost journal sales.

OncologySTAT: free access to journal articles from Elsevier oncology journals

Earlier this month, Apple announced the productivity suite iWork 08 for Macintosh users. iWork 08 includes Numbers, a new spreadsheet application and updated versions of the presentation and word processing applications Keynote and Pages.

Earlier this month, Apple announced the productivity suite iWork 08 for Macintosh users.

iWork 08 ready for scientists?

The Force2021 conference will take place from December 7-9. The conference will be virtual, and registration is free. And we will again be hosting a Force2021 hackathon, as co-located virtual event on December 6 and December 10. We will meet for four hours each (1 PM - 5 PM GMT) and will communicate via Zoom.

Join us for the Force2021 Hackathon

This week the Rogue Scholar science blog archive experienced major upgrade pains, and Rogue Scholar search became unavailable from Tuesday until Thursday. I tried to upgrade to a pre-release version (13.0.0b4.dev0) of the InvenioRDM repository software, and ran into multiple issues. Going back to the previously installed v12.1.0 took longer than anticipated, mainly because of issues with the Opensearch index.

Rogue Scholar upgrade pains

In the last few months we have seen an ever increasing number of new social networking (Web 2.0) sites for scientists. Good Web 2.0 tools for scientists primarily try to solve a problem. But by adding a social aspect, they will gain useful features that would otherwise not be possible. Eva Amsen has recently written a great blog post about this1.

In the last few months we have seen an ever increasing number of new social networking (Web 2.0) sites for scientists. Good Web 2.0 tools for scientists primarily try to solve a problem. But by adding a social aspect, they will gain useful features that would otherwise not be possible.

Mendeley: Interview with Victor Henning

This week I launched Commonmeta, a new scholarly metadata standard described at https://commonmeta.org. Commonmeta is the result of working on conversion tools for scholarly metadata for many years. One conclusion early on was that these conversions are many-to-many, so it becomes much easier to have an internal format that is the intermediate step for these conversions. Commonmeta is inspired by two initiatives: Codemeta and Commonmark.

This week I launched

 Commonmeta

, a new scholarly metadata standard described at https://commonmeta.org. Commonmeta is the result of working on conversion tools for scholarly metadata for many years. One conclusion early on was that these conversions are many-to-many, so it becomes much easier to have an internal format that is the intermediate step for these conversions.

Announcing Commonmeta

One question I have increasingly asked myself in the past few years. Meaning Can I run this open source software  using Docker containers and a Docker Compose file? As the Docker project turned ten this spring, it has become standard practice to distribute open source software via Docker images and to provide a Docker Compose file to run the software together with other dependencies.

One question I have increasingly asked myself in the past few years. Meaning  As the Docker project turned ten this spring, it has become standard practice to distribute open source software via Docker images and to provide a Docker Compose file to run the software together with other dependencies. The Awesome Compose project has collected many examples, and all you need is a docker-compose.ymlfile and a recent installation of Docker, e.g.

Does it compose?

In one of my first blog posts (before I joined Nature Network) about a year ago I wrote about the American Society of Clinical Oncology (ASCO) 2007 Meeting. I was surprised that only a handful of blogs reported about the event, one of the largest and most important meetings for clinical cancer research. One would think that blogging and scientific meetings would be a natural combination.

Scientific meetings need more bloggers

In the comments on Monday’s blog post about the Markdown for Science workshop, Carl Boettiger had some good arguments against the proposal for how to do citations that we came up with during the workshop. As this is a complex topic, I decided to write this blog post. Citations of the scholarly literature are an essential part of scholarly texts and therefore have to be supported by scholarly markdown.

Citations in Scholarly Markdown

Zotero is a reference manager built as an extension of the Firefox web browser. The best introduction to Zotero is probably this short video. Last week the newest version (1.5 beta) was announced on the Zotero blog. Among the most exciting new features is the synchronization of library data with the Zotero server, which in the future will allow a lot of interesting social features.

Zotero: Interview with Trevor Owens

Four years ago I wrote a blog post about component DOIs. It is time to revisit the topic, in particular since our approach to citing data associated with a publication has changed since 2011. Component DOIs are explained in the CrossRef Help System: DOIs may be assigned to items that are part of a journal article, book chapter, or any other content item.

Four years ago I wrote a blog post about component DOIs. It is time to revisit the topic, in particular since our approach to citing data associated with a publication has changed since 2011. Component DOIs are explained in the CrossRef Help System: Component DOIs are DOIs, i.e. persistent identifiers that link directly to the resource in question, e.g. a figure in a publication.

Component DOIs Revisited

At the beginning of the month Google, Bing and Yahoo announced schema.org, a new initiative for structured markup on the web. Richard MacManus responded with a critical piece at ReadWriteWeb (Is Schema.org really a Google Land Grab?), mainly criticizing that the initiative didn’t use RDFa and didn’t seem to have consulted with the web standards body W3C.

Is Schema.org about a technical standard or about something else?

This was the title of the session with

 
 Geoff Bilder
 

,

 
 Gudmundur Thorisson
 

and myself at the Science Online London Conference last Saturday. Geoff first introduced the ORCID initiative, including several  principles. We then talked about two use cases for ORCID.

ORCID as unique author identifier: what is it good for and should we worry or be happy?

Following recent announcements of the commonmeta standard for scholarly metadata and a Python package that converts several metadata formats (commonmeta-py), today I am happy to announce commonmeta-ruby, a Ruby gem and command-line tool to convert scholarly metadata using commonmeta as the internal format.

Announcing commonmeta-ruby

The science blog archive Rogue Scholar is becoming a German non-profit membership organization in 2026. This will help with the governance and sustainability of Rogue Scholar. But what can be the incentives to become a Rogue Scholar member, and under what conditions?

The science blog archive Rogue Scholar is becoming a German non-profit membership organization in 2026. This will help with the governance and sustainability of Rogue Scholar. But what can be the incentives to become a Rogue Scholar member, and under what conditions?Personal vs. Organizational membership  Membership will be open to all legal entities that support the mission and objectives of Rogue Scholar.

Incentives for Rogue Scholar membership

Are you tired of writing a paper, based on real experiments? SciGen could come to the rescue, at least if you do computer science research. SciGen is a program that creates random papers, complete with results, discussion, graphs and references. Some of these random papers have been accepted at conferences or even for publication. SciGen is of course a hoax.

Your next paper could be computer-generated

Reinventing Discovery, the book by Michael Nielsen we all have been waiting for, has finally been published on Friday. Today I flew to Boston for the Microsoft Research eScience Workshop: Transforming Scholarly Communication, and reading the book on the plane was the perfect preparation for the workshop. Michael says in the book: I wrote this book with the goal of lightning an almighty fire under the scientific community.

Reinventing Discovery, the book by Michael Nielsen we all have been waiting for, has finally been published on Friday. Today I flew to Boston for the Microsoft Research eScience Workshop: Transforming Scholarly Communication, and reading the book on the plane was the perfect preparation for the workshop.

Book Review: Reinventing Discovery by Michael Nielsen

Today I am happy to announce an important milestone for the Rogue Scholar science blog archive. Starting November 1st, all blog posts from participating blogs will automatically be archived by the Internet Archive. Front Matter has signed a contract with Internet Archive to use their Archive-It service, and archiving will start in November.

Starting November, all Rogue Scholar blog posts will be archived by the Internet Archive

Last month (shortly after ScienceOnline2010)

 
 David Crotty
 

wrote in a blog post Science and Web 2.0: Talking About Science vs. Doing Science: The blog post is required reading for everybody interested in science and Web 2.0 and has attracted a lot of thoughtful comments (on the blog and on FriendFeed). In another discussion

 
 Thomas S
 
 ö
 
 derquist
 

from the Medical Museion in Copenhagen reminded me that there

Chances and problems of doing science online

Another guest post by Alex Knoll reporting from the German Genetics Society Meeting in Cologne. Saturday had two more sessions before the end of the meeting. Irina Stancheva from the Wellcome Trust Centre for Cell Biology at the University of Edinburgh started us into the day with a talk on epigenetics in mouse development. One form of epigenetic silencing is methylation of cytosine bases in DNA.

Another guest post by Alex Knoll reporting from the German Genetics Society Meeting in Cologne.
 

Saturday had two more sessions before the end of the meeting. Irina Stancheva from the Wellcome Trust Centre for Cell Biology at the University of Edinburgh started us into the day with a talk on epigenetics in mouse development. One form of epigenetic silencing is methylation of cytosine bases in DNA.

German Genetics Society Meeting 2009: Session VI

Another guest post from Alex Knoll reporting from the German Genetics Conference in Cologne. Dusko Ehrlich fom Jouy en Josas in France started off the second session of the meeting. He is working with the MetaHIT project, which tries to do a metagenomic analysis of the human intestinal tract. This is interesting because each individual human carries about ten times more microbial cell in the gut than there are human cells in the whole body!

Another guest post from Alex Knoll reporting from the German Genetics Conference in Cologne.
 

Dusko Ehrlich fom Jouy en Josas in France started off the second session of the meeting. He is working with the MetaHIT project, which tries to do a metagenomic analysis of the human intestinal tract.