Transparent research starts with an unambiguous parts list. To help promote the wider use of identifiers and recognized symbols in biological research, FlyBase (with input from other model organism databases) is developing a resource for tracking and reporting reagents in a more standardized way, aiding curation into research databases.

The GSA journals are now encouraging authors to use this Reagent Table and to provide input to help the community develop and improve the concept.

The Reagent Table is provided as a spreadsheet template, a format that is convenient and flexible for the researcher, easily used by readers of research publications, and allows bulk downloads for database curation. The table is designed for use in the lab, as a research project is conducted. Unambiguous identification of not only reagents, but the specific genes studied is particularly helpful for genetic and genome databases, as well as for other researchers, helping avoid confusion around genes with similar names or symbols.

The template, detailed instructions, and an example file are available in the journals’ Instructions for Authors. Please send feedback and suggestions to genetics-gsa@thegsajournals.org.

Do you have whole genome sequence (WGS) data burning a hole in your pocket? Many high-quality WGS datasets languish unpublished and undescribed because they may not always—in isolation—reveal substantial new biological insights. However, the editors of G3: Genes|Genomes|Genetics recognize that WGS data on strain variation, comparative analysis of different model organism species, and other rich analyses are most valuable when made available to the research community in an accessible format. To enhance the sharing of such data, G3 is pleased to offer a new article type: Genome Reports. The Genome Report format is succinct and follows a structured template (details here) designed to make it fast and easy for authors to submit, for reviewers to rapidly assess, and for readers to easily understand the report and its results.

Criteria for acceptance in this category include:

• usefulness of the report—will the information provided assist future genetic investigations?
• quality of the results—was the WGS well performed?
• completeness—are the results comprehensive?
• author’s interpretation of results—are the results of the WGS lucidly interpreted for the reader?

The amount of new information needed to warrant publication will vary by organism/system; for example, sequencing a couple of new isolates of Saccharomyces cerevisiae, for which there is already substantial sequence variation information available, would likely not be useful enough to warrant standalone publication in this format.

The first Genome Report was published in the December issue of G3. It describes genome data from two wild-derived mouse inbred strains that were among the top 10 inbred strains recommended for resequencing based on their potential to increase the catalog of known mouse variants. The work expands the number of wild-derived inbred genomes in the Mus genus from six to eight. A second Genome Report has just been accepted and made available in Early Online format. It describes the genome of the bacteria that causes “foothill abortion” in pregnant cows and the use of reverse vaccinology to identify antigenic proteins that may be candidates for future recombinant vaccine development.

Learn more about the format at our Instructions for Authors and get ready to submit your valuable WGS datasets!

CITATIONS

Andrew P. Morgan, John P. Didion, Anthony G. Doran, James M. Holt, Leonard McMillan, Thomas M. Keane, and Fernando Pardo-Manuel de Villena Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers

G3: Genes|Genomes|Genetics 6(12), 4211-4216 doi:10.1534/g3.116.034751

http://g3journal.org/content/6/12/4211.full

Bryan T. Welly, Michael R. Miller, Jeffrey L. Stott, Myra T. Blanchard, Alma D. Islas-Trejo, Sean M. O’Rourke, Amy E. Young, Juan F. Medrano, and Alison L. Van Eenennaam Genome Report: Identification and Validation of Antigenic Proteins from Pajaroellobacter abortibovis Using De Novo Genome Sequence Assembly and Reverse Vaccinology

G3: Genes|Genomes|Genetics Early Online December 30, 2016, doi:10.1534/g3.116.036673

http://www.g3journal.org/content/early/2016/12/28/g3.116.036673.full.pdf+html

Got a hot manuscript or a burning question for a GENETICS or G3 editor? Just want to talk about scholarly publishing in general? Here’s how you can track down an editor at The Allied Genetics Conference this week:

Watch out for ribbons

GENETICS and G3 Editors will be wearing silver “Editor” ribbons on their name tags so you can spot them at a distance.

Go to a “Meet the Editors-in-Chief” session

GENETICS Editor-in-Chief Mark Johnston and G3 Editor-in-Chief Brenda Andrews will be available at the GSA Central Theatre in the exhibit hall at the following times:

Wednesday, 7/13/2016, 10:00-10:30PM  (Mark Johnston only at this time)

Saturday, 7/16/2016, 10:30-11:00AM

Go to a “Meet the Editors at the Booth” session

Editors will be available for questions at GSA Central at the following times:

Thursday, 7/14/2016 2-2:30 PM

Friday, 7/15/2016 2-2:30 PM

Join the conversation at the Editors’ Panel Discussion and Roundtable

This is an excellent opportunity for graduate students, postdoctoral fellows and undergraduate students to have informal conversations with journal editors about the peer-review and scientific publishing process in general. There will be brief presentations by GENETICS Editor-in-Chief Mark Johnston, G3: Genes|Genomes|Genetics Editor-in-Chief Brenda J. Andrews, and GSA Journals Executive Editor Tracey DePellegrin. This will be followed by roundtable discussions with rotating editors from a variety of journals, so that each participant gets discussion time with multiple editors.

Friday, 7/15/16 12:00-1:30 PM North Tower: Harbor Beach/Marco Island

Drop by the GSA booth and talk to editorial staff

Can’t find the Editor you’re looking for? Not sure who can answer your question? Have a question about the submission procedure or the peer review process? Ask a Staff member at GSA Central.

Attend an editor’s talk in the GSA Central Theatre

Want advice on promoting your research or writing great journal article titles? Catch presentations by GENETICS Editor-in-Chief Mark Johnston and GSA Journals Executive Editor Tracey DePellegrin at the GSA Central Theatre. There will be a variety of other informative talks at the Theatre, check out the schedule below:

You may have seen that recently several publishers signed an open letter committing to requiring ORCID iDs for at least the corresponding authors of accepted papers. Perhaps you’ve submitted a grant application to one of the funders now requiring ORCID iDs for grantees. Or maybe you’ve been asked—or required—to use your ORCID iD in one or more of your institution’s systems. Why all the fuss, you may be wondering. What’s the big deal about ORCID? Why do I need yet another identifier, when I already have more than enough to keep track of?

Here are what we believe are some of the most compelling reasons to get—and, most importantly, use—an ORCID iD.

1. Distinguish yourself. If you share your name with other researchers—in your own or another field—an ORCID iD will help distinguish you from them. It can also help you bring together all of the names you have used to publish your work. Uniquely identifying you and correctly connecting you with your research activities is far from straightforward. The screenshot below, for example, shows a co-author tag sent to Karin Wulf, Director, Omohundro Institute of Early American History and Culture and Professor of History at the College of William & Mary—a relatively uncommon name and about as far as you can get from chemistry! This misattribution would not have happened if the actual authors had used ORCID iDs when submitting their paper.

2. Your lifelong digital name. Even if you have an unusual name, it can still be difficult to correctly identify and connect you with all your activities and affiliations. Throughout the course of your career, you may change your name, publish under different versions of it, or have it transliterated into other alphabets. You may also change organizations or countries, fields, or even disciplines. But you still want to be uniquely identifiable and to stay connected with your body of work. Your ORCID iD stays with you throughout your professional life, ensuring that you and your research contributions stay connected.

3. You’re in control. ORCID is researcher-centric, built on principles of researcher control and privacy. You register for an iD yourself and decide which information to connect to it, including what to make public, what to share with trusted parties, and what to keep private. You choose how often—if at all—you get notifications. And you can change your permissions, settings, or delete items at any time.

4. “Enter once, re-use often.” Our goal is to minimize—and ultimately eliminate—rekeying of data in multiple systems, saving you time and reducing the risk of errors. We do this by developing open tools and services that allow you to connect your ORCID record with other systems you use (grant application, manuscript submission, and research information management systems, for example). Once connected, you can grant permission to those systems to update your ORCID record.

5. Automatic updates. Even better, in some cases you can opt for these updates to happen automatically AND your trusted organizations can opt to be notified when new items are added to your record, saving you reporting time. One great example is Crossref’s new auto-update functionality. Crossref creates DOIs for publications and, as long as you use your ORCID iD during manuscript submission and your publisher passes it along in the metadata, Crossref can now automatically update your ORCID record when your paper is published. You simply have to grant permission once, and they will enable updates for any publication and any publisher. Look out for an email from update@notify.orcid.org.

6. More than just publications. As well as easily connecting your publications to your ORCID record, you can also connect peer review activities, datasets, grants, and more. Life scientists are especially keen to connect datasets and peer review to their ORCID record, which is good news, since both are easy to do. DataCite’s Search & Link wizard already allows you to connect your existing dataset DOIs to your record, and they are launching auto-update functionality similar to Crossref. And last October, we launched new functionality to enable acknowledgement of peer review activities, which has been launched by several publishers and is in the works at some funding organizations.

7. Quick, easy, and free. Registering for an ORCID iD couldn’t be easier—all we require is one version of your name, a valid email address, and a password. We encourage you to include all versions of your name (any character set), your affiliation(s) and research contributions. You can find out more about what to do once you’ve got an ORCID iD—and why—here.

8. Open, community-led. ORCID is non-proprietary, which means you can use it in many of the systems you already use, including grant applications systems at Wellcome Trust, the SciENcv system at NIH, manuscript submission systems at over 2500 journals, and your local university or research institute research profile system.  You can also easily connect your information held in author profile systems such as ResearcherID and Scopus Author ID to your ORCID record. We have a public API and make all our documentation and resources freely available under a Creative Commons CC0 license. And because we are a community-led non-profit organization, you can be sure that we will always have the best interests of the research community at heart.

If you don’t already have an ORCID iD we very much hope that you’ll consider joining 2m+ colleagues globally, register for one today and start using it right away!

Alice Meadows is Director for Community Engagement and Support at ORCID. In this role, she develops and implements ORCID’s communication plan and leads its support services team. Her primary role is to broaden awareness of the organization and its services and programs and support adoption by key stakeholders and audiences.

A big thank you to ORCID Executive Director Laurel L. Haak for her help with this post.

You slave over writing your paper, trying to make sure that the introduction sets up a compelling story, that the results provide clear and convincing evidence for your conclusions, and that your discussion of what it all means makes sense. You and your co-authors edit relentlessly, passing the manuscript back and forth, improving it with each round of tweaks.  When you realize the returns are diminishing, you decide the paper is ready to submit for publication.

But wait: what’s the title? You quickly write down what the paper is about — “Studies on the chemical nature of the substance inducing transformation of pneumococcal types: Induction of transformation by a desoxyribonucleic acid fraction isolated from Pneumococcus type III” — head to the journal’s submission website, dash off a cover letter, upload data to Dryad and FigShare, and click the submit button.

The first thing the editor reads is the title. She scratches her head and moves on to the abstract and cover letter to learn what the paper is about. She sees that it looks interesting and potentially significant, so she invites an expert to review the manuscript. He sees the title, scratches his head, and moves on to the abstract and cover letter to learn what the paper is about. He realizes there might be something interesting there, so he agrees to review it. The paper receives good reviews and eventually gets published. A reader comes across the title in the journal’s table of contents. He scratches his head and moves on to the next title.

Some say the abstract is the most important section of a paper because it’s the part that most people read and is widely available. But an even greater number of people will lay eyes on the title. A carefully crafted title can attract readers to your paper; a difficult or dull one is likely to turn them away.

It seems obvious that titles should be clear, concise, and compelling, but I admit to sometimes not having taken them seriously enough with my own papers. After all, titles should be easy to write:  they’re just a handful of words. But I became hyperaware of the importance of interesting, inviting titles once I started helping put together the Table of Contents for GENETICS each month.  I now frequently give authors suggestions for improving their titles to increase the impact and readership of their papers. Here are a few suggestions for composing titles that I’ve come up with along the way:

1. Don’t bury the lede. Start with the topic of the paper, not with the name of the gene or organism you studied. A title such as
   

   “Fibulin-1 interacts with type IV collagen and antagonizes GON-1/ADAMTS in shaping the C. elegans gonad”

   is unlikely to attract potential readers who don’t know what Fibulin-1 and GON-1/ADAMTS are (which is almost everybody), and “type IV collagen” will generate interest in only the most special of specialists.  Something like

   “Shaping of tissue architecture in the C. elegans gonad by interactions among fibulin-1, type IV collagen, and the ADAMTS extracellular protease”

   is more likely to snare a reader because the first thing she sees is “tissue architecture”, which sounds like an interesting topic. A title that begins with

   “The C. elegans transcriptional regulators LIN-15A and LIN-56 interact and function redundantly……….”

   will attract readers interested only in C. elegans, and even among them the only ones likely to look at the abstract are those who know something about LIN-15A and LIN-56. Put the specific stuff as far into the title as possible, after you’ve hooked the reader with terms of more general interest. Better yet, leave the specific stuff out if you can.

2.    Entice the reader. Make what you learned seem exciting (I assume you, the author, think it is exciting).
   

   “Transcriptome and Genetic Analyses Reveal that Abc1 and Def2 are Required for Glucagon Secretion”

   could become

   “Glucagon secretion requirements revealed by transcriptome and genetic analysis of glucagon-producing cells.”

   Readers are more likely to look at your paper if the first thing they see makes them think it will offer some insight into an interesting topic, rather than just some analysis of a bunch of data.

   “A novel method of genetic selection in yeast identifies the DNA binding site of NGFIB”

   entices the reader with the prospect of learning about a new, possibly innovative method.  By contrast, the real title of the paper—

   “Identification of the DNA binding site of NGFIB using genetic selection in yeast”

   —seems to offer (yawn) just another binding site.

3. Avoid jargon. Jargon is hard to avoid in technical publications, but you should do your best to purge it from the title.
   

   “FLP-21/NPR-1 Signaling and the TRPV Channels OSM-9 and OCR-2 Independently Control Heat Avoidance in Caenorhabditis elegans”

   is better as something like

   “Regulation of Heat Avoidance in Caenorhabditis elegans by Peptide Signaling and Transient Receptor Potential (TRP) Channels.”

   Jargon turns off the majority of readers, who may not be familiar with the specialized terms. Avoid unnecessary abbreviations and acronyms too.

4.    Be concise. Readers have a limited attention span. Instead of
   

   “The Maize Zea mays stunter1 Mutation Causes a Reduction in Gametophyte Size, Has Maternal Effects on Seed Development, and Reveals that Endosperm Development is not Essential for Early Embryo Development”

   try something like

   “Effects on gametophyte development in maize of a maternal effect mutation in stunter1.”

   Thirteen words are more digestible than 30. In fact, most readers are unlikely to read past about a dozen words before their eyes wander away from your title.

5.    Don’t give away the ending. Some authors treat the title as a one-sentence abstract, but I think that’s a mistake. The purpose of the title is to entice readers with the question under investigation so they’ll want to read more, not to tell the whole story. Don’t give the conclusion of your story in the title. So,
   

   “MCM-related precondition gene mei-218 inhibits lig4-dependent repair and promotes checkpoint activation during Drosophila meiosis”

   might be better as

   “Multiple barriers to non-homologous DNA end joining during meiosis in Drosophila.”

   That makes me want to read on to learn what the multiple barriers are. And the declarative verbs that came into vogue among molecular biologists in the 1970s should be avoided, in my opinion.  Titles such as

   “The Type VI Secretion TssEFGK-VgrG Phage-Like Baseplate Is Recruited to the TssJLM Membrane Complex via Multiple Contacts and Serves As Assembly Platform for Tail Tube/Sheath Polymerization”

   gives me the impression that I’ve just learned all I want to know about the paper. Leave the reader in some suspense, wanting to read on to see how the story ends.

Keep these suggestions in mind when you’re composing titles of your papers and I expect you’ll increase the impact of your publications. If Oswald Avery had done so, his paper (whose title is in the 2nd paragraph above) might have been titled

“Desoxyribonucleic acid as the carrier of heredity”

which might have brought a wider readership, and—who knows?—maybe the Nobel Prize he deserved.

Footnote:  I thank various GENETICS authors for donating their titles in progress (TIPs) to this post.

Kevin Ahern and Indira Rajagopal, both from the Department of Biochemistry and Biophysics at Oregon State University, described the process of creating an interactive e-textbook in biochemistry while presenting at the Gordon Research Conference on Undergraduate Biology Education Research in the summer of 2015. G2G asked them about their experience writing and publishing and they offer advice to anyone contemplating e-book authorship.

“Cover” of Ahern and Rajagopal’s e-book

The term “Open Educational Resources” (OER) was first adopted by the United Nations Educational, Scientific and Cultural Organization (UNESCO) in 2002, at a forum on the impact of open courseware in making higher education more accessible worldwide.  A definition at the OER Commons states that “Open Educational Resources are teaching and learning materials that are freely available online for everyone to use, whether you are an instructor, student or self-learner.”

As faculty at a land-grant university, we have witnessed the effects of the rising cost of higher education as our students struggle to complete college in a timely manner, even as they take on increasing amounts of debt. OERs hold the potential to help ease the burden for students, especially those of modest means.

This is the story of Biochemistry Free and Easy, an OER e-textbook for introductory biochemistry that we have created and distributed worldwide since 2012. We did not originally envision the book as a free e-textbook; initially, we  were writing a simple, introductory text focusing on basic biochemistry, to be published at low cost as a print book by a small start-up publisher. We quickly discovered that the publisher did not have the resources to create a quality publication and the price they wanted to charge was much higher than we had been led to believe. Our discussion of these issues with the managing editor led a termination of our agreement with the company, leaving us with a book with no publisher that still needed figures. Kevin obtained a grant to pay a graphic arts student to create figures for what we  assumed would be a print book.

Then, on January 19, 2012, a new software tool was released that changed everything for us. iBooks Author is an Apple product that allows one to easily create electronic books readable on an iPad or as PDF files for a personal computer. At the same time, Apple created a section of the iBooks marketplace for publishing and distributing iPad (and Macintosh)-based textbooks. Apple normally retains 30% of the book’s cost and leaves the author with 70%, but if authors do not charge for their book, then Apple distributes it cost-free. We realized at once that we could use iBooks Author to create an attractive e-book that could incorporate the advantages of electronic media and distribute it worldwide at no cost, since we did not intend to charge for it.

Anyone who has used other page layout programs will readily be able to create a book with iBooks Author. With it, we could blend figures and text easily via drag and drop and we could also integrate media, such as audio, video, and rotatable 3D models. Working in the evenings over about a two-month span, we completed the layout and uploaded our book to the iBookstore for approval, which came on August 2, 2012. At that point, the iPad version was released, followed shortly later by the PDF version (hosted by our own department). In early 2015, a Kindle version followed.

As of today, over 140,000 copies of the book have been downloaded by students all over the world and demand remains quite strong. Along the way, we learned a good deal about what it takes to make a successful OER e-book:

1. Successful OER e-books must be accurate, understandable, easy to use/read, and (increasingly) interactive. Some students like to be “told” the relevant information and others like to discover/explore it. A successful book must balance these perspectives.
2. Figures are a challenge and can be expensive. Graphic arts students can often be hired on campus to save money. All artwork is best created as vector-based figures, since these can be scaled and readily converted to JPEGs or PNGs. There are also many high quality figures available in the public domain (and under Creative Commons licensing, if used appropriately).
3. iBooks Author is an Apple product. We are unaware of a similar, easy-to-learn tool for making Android tablet-based content. Though PDFs can be read on almost all tablets and personal computers, that format lacks the ability to handle multi-media, which is important in an electronic book. If software to create similar content for other platforms were available this could extend the reach of OER e-books.
4. Success with an OER book requires that people learn about it. Many faculty are not aware of OERs that may be useful or relevant to their courses. This can limit the use of such resources in college classrooms. Traditional publishers work from the top down, by paying a large sales staff to connect with instructors. Our book has been a bottom-up effort, since students are the ones who discover our books first. Consequently, there have been relatively few adoptions of our book for courses, since most professors only learn of the book after their students show it to them. One very valuable source of free publicity has been YouTube where Kevin has numerous video lectures that are quite popular with students. Each video lists a link to the free textbook and this is the most common way students have found out about the book.
5. Authors of OER books do not receive financial rewards, at least not directly. We have advanced in our careers (promotions, raises) as a byproduct of the success of our book, but there are no royalties for a free book. On the other hand, there is enormous value to contributing to making education accessible to as many people as possible and that, in fact, has been our primary motivation and source of satisfaction.

We are currently working on another OER book, tentatively titled “Biochemistry Free for All.” It will provide a considerably more advanced coverage of biochemistry than the first one and will be distributed through the OSU Press (free as an e-book and provided at cost for print-on-demand hard copies).

Indira Rajagopal (left) and Kevin Ahern (right)

Dr. Indira Rajagopal is a Senior Instructor for the Oregon State University  (OSU)  Department of Biochemistry and Biophysics. She received her PhD in Biochemistry from the Indian Institute of Science (Bangalore, India).
Dr. Kevin Ahern is a Professor in the Department of Biochemistry and Biophysics at Oregon State and makes all of his lectures available on YouTube. He received his PhD in Biochemistry and Biophysics from OSU.

The views expressed in guest posts are those of the authors and are not necessarily endorsed by the Genetics Society of America.