All posts by guest

Open Access Month – OA Creates Momentum for Discovery

October is Open Access Month. Throughout the month, guest contributors will present their perspectives on the value of open access to research, scholarship and innovation at The University of Texas at Austin.

This installment provided by Rayna Harris (ORCID ID:0000-0002-7943-5650), PhD Candidate, Cell and Molecular Biology.

Open access publishing is critical for ‘daisy chain’ reading of scientific papers

Rayna Harris.
Rayna Harris.

Whenever I read a scientific paper, there is almost always a citation that grabs my attention and begs to be read. I love it when I can click on a citation and then read the full text. This ‘daisy chain’ process of citation searching (where the second paper leads me to a third paper, which leads me to a forth, and so on) gives me a great appreciation for all the previous research that contributes to current knowledge.

Figure 1. An example of citation searching or ‘daisy chain’ reading of scientific papers. In this example, McKiernan et al. 2016, cite Brenner 1995, who refers to Watson & Crick 1995. All these papers are open access and can be read by all.
Figure 1. An example of citation searching or ‘daisy chain’ reading of scientific papers. In this example, McKiernan et al. 2016, cite Brenner 1995, who refers to Watson & Crick 1995. All these papers are open access and can be read by all.

When my citation search leads me to a paper that is not open access, I get frustrated because its halts the excellent momentum I had going for gaining new new knowledge. There is a saying in my lab that “if the research isn’t published it doesn’t exist” because it has not been disseminated to broader audiences. I would like to modify this quote to say “if the research is not published and open access then it doesn’t exist” because pay-walled papers are not freely discoverable.

Open access publishing is necessary for dissemination of ideas because it gives readers the ability to read any paper anytime anywhere. My hope is that one day I will publish a scientific paper that 1) is open access, 2) cites only open access papers, 3) which in turn cite only open science papers, and so on. This way, future readers can daisy-chain their way through the history of research that lead to current understanding.

 

Open Access Month – OA to Spur Innovation

October is Open Access Month. Throughout the month, guest contributors will present their perspectives on the value of open access to research, scholarship and innovation at The University of Texas at Austin.

This installment provided by Dr. Maryjka B. Blaszczyk,Postdoctoral Research Associate, Department of Anthropology.

A need for open access to research materials to spur new discoveries in biological anthropology

Dr. Maryjka B. Blaszczyk.
Dr. Maryjka B. Blaszczyk.

A major aim of research in biological anthropology is to understand how humans have ended up looking and behaving the way that they do. To understand the evolution of our body form, anthropologists look at fossils. Behavior, however, does not fossilize, and so we turn to studying our closest living relatives, the nonhuman primates, preferably in their natural habitats where they have to deal with selective pressures such as avoiding predators and finding enough food to eat. Primate behavior field data are hard-won, involving substantial investments of time and resources. Apart from jumping through logistical hoops such as obtaining permits and building relationships with local stakeholders in far-flung locales, establishing a new field site for behavioral fieldwork involves months if not years of patiently following wild primates around to habituate them to researchers’ presence. Once habituated, data collection begins, with blood, sweat, and tears invariably spilt as one accumulates precious hours of detailed behavioral observations on this group of primates at this place and particular time.

These investments are one reason given by field primatologists as justification for closely guarding their data. Another is the unique insights they have into the lives of their study animals, having spent hours upon hours of observation time with them. Some primatologists argue that researchers not familiar with their study site and animals may misuse the data if they were to make it widely available, subjecting it to improper analyses or not accounting for information about the study site/animals that is known only to researchers who have worked there. Researchers also generally have many ideas for secondary analyses of their data that they plan to get to in the future.

Each of these arguments is by no means specific to primate behavioral ecology, with very similar arguments having been made, for example, by medical researchers working with clinical trial data. Of course, clinical trial data has a substantially higher status (given its applications for human health and welfare) than primate behavior data, and arguments about the costs and benefits of trial data sharing have been ongoing in high profile forums for several years. Data sharing advocates point to benefits such as new discoveries, better metanalyses, and correction or confirmation of findings in the scientific record, which they argue far outweigh potential risks such as incorrect analyses or data misuse. We all know researchers who have been sitting on data for years (even decades) with plans for secondary analyses, many of which they will never find the time to conduct and publish. In the case of primate field data collected on a specific population at a specific place and point in time – and frequently on endangered primates living in rapidly changing habitats – these data cannot be reproduced, so it is a double shame that they may never make it into the scientific record.

Primate behavioral ecologists are included in Anthropology departments because comparative studies on primate behavior illuminate the ways in which humans differ from and are similar to our closest kin, allowing us to better understand the evolutionary ecology of our lineage.  However, many comparative studies are hampered by poor descriptions of how data in primate field studies were collected and processed, and many large-scale comparative studies cannot be undertaken unless raw data itself is made available. Behavioral ecologists should take a page out of their molecular primatology colleagues’ playbooks, where publication of genetic data alongside scientific articles is the rule. This type of data sharing has enabled large-scale comparative phylogenetic studies that have given us a rich understanding of primate evolution. It is time for primate behavioral ecologists to catch up and to make sharing of data as well as associated behavioral and ecological data collection protocols the norm. Who knows what insights await us.

Open Access Month – Open the Data

October is Open Access Month. Throughout the month, guest contributors will present their perspectives on the value of open access to research, scholarship and innovation at The University of Texas at Austin.

This installment provided by Spencer J. Fox (ORCID ID: 0000-0003-1969-3778), PhD candidate focusing on computational epidemiology.

Spencer J. Fox.
Spencer J. Fox.

Three years ago, I was choosing the next research direction for my PhD. I was interested in two subjects and had found a journal article in each to build upon. I thought to follow the computational biologist’s path of least resistance: pursue the paper whose results I could reproduce first, as that represents an important first step. One of the papers had published a repository with all of their data alongside working code for analyzing it, while the other had simply stated: “Data available upon request” with no reference to code used for the analyses.

Being a naive graduate student, I politely reached out to the authors of the second study to obtain their data and inquire about their code. In return, I received a scathing email filled with broken links to old websites, excuses about proprietary data, and admonishment for having asked for “their” code: “any competent researcher in the field could replicate our analysis from the information within the manuscript.” I was stunned.

While expressing my frustration to my peers, I found that their requests had also been met with equal hostility and degradation from scientists in their respective fields. When data or code had been provided – usually after months of negotiations – cooperation came with heavy stipulations in article authorship, time-stamped embargos, or permissible analyses. Clearly, it’s not enough to rely on researchers to act in good faith.

The unfortunate truth is that the onus falls on journals to enact real change. Many major journals now require that raw data be deposited in permanent online repositories like Dryad1. This has improved data sharing, but is only half the battle and simply provides the likeness of reproducible research. I have spent weeks reproducing someone’s analysis using their provided data and code. It would have been impossible without both. Simply put, freely available code – even if messy and difficult to follow – provides an invaluable foundation for future researchers to build upon, and all journals should require that both analysis code and data accompany a manuscript.

Too many conscious and subconscious coding decisions are made over the course of a project that even minor decisions early on present serious stumbling blocks for researchers trying to reproduce results. Differences in mundane behaviors between programming languages, versions, library functions, and self-written pipelines can have drastic implications on end results. A great example of this is the inadvertent errors in one fifth of genomics papers attributed to Microsoft Excel use2.

Finally, while ultimately it is the researcher’s responsibility to provide code alongside a manuscript, there are tangible incentives for doing so: citations. Open access manuscripts and those that provide their data receive more citations3,4, and the same likely applies to providing analysis code. After debating between those articles three years ago, I alone have cited the reproducible paper in two separate publications. How many other potential citations are lost “upon request”?


Citations

  1. http://datadryad.org/
  2. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1044-7
  3. https://elifesciences.org/articles/16800
  4. https://peerj.com/articles/175/

Open Access Month – Open Educational Resources in Biology

October is Open Access Month. Throughout the month, guest contributors will present their perspectives on the value of open access to research, scholarship and innovation at The University of Texas at Austin.

This installment provided by Sata Sathasivan, Senior Lecturer, Biology Instructional Office.

K.Sata Sathasivan.

I have been using open educational resources (OER) in biology as supplemental instructional sources for many years. These included animations, videos, simulations and public databases of DNA and protein. These resources are constantly evolving and they complement well with any level of teaching.

Recently, I started using a biology textbook published by Open Stax based at Rice University for my introductory biology classes successfully. While a publisher’s popular textbook may cost the students up to $250 each semester, OpenStax textbooks are free to download a PDF and have a nominal cost ($40) for printed versions. Several students liked this free textbook and I received only a few complaints about the inadequacies of this textbook to explain a particular concept. Overall, it was well received by the students and they found this very helpful.

This free textbook can be supplemented with other open educational resources that can be found online in various sites such as https://www.oercommons.org, and if you want to explore more OER sites, check this site.

The only concern that I have about OERs is the time it takes to check them for quality and consistency with your teaching, and the time involved in making the structure for them to be seamlessly integrated into the course.

Exhibit Features Black Queer Studies Collection

Exhibit of items from the Black Queer Studies Collection.
Exhibit of items from the Black Queer Studies Collection.

Written by Hayley Morgenstern, Graduate Research Assistant/Ask a Librarian Intern

The creation of the Black Queer Studies Collection (BQSC) by former librarian Kristen Hogan in collaboration with faculty member Dr. Matt Richardson responds to the need to make content that is marginalized within classification systems more accessible for scholarship.

One of the first special collections of its kind in the U.S. South, the BQSC is a designated virtual collection that seeks to address discoverability issues surrounding holdings in the area of African and African Diasporic Lesbian, Gay, Bisexual, Transgender, and Queer Studies. Since standard Library of Congress subject headings are limited in addressing gender and sexual identity, adding a local note to items in the catalog allows materials addressing black queer content to become accessible through a keyword search. The creation of the collection to meet a research need of students and faculty exemplifies the vision of the library as a research ecosystem created through user-focused innovation, collaboration, and expertise.

Over 750 items exist in the collection that spans multiple branches of the library system from the Perry-Castañeda Library, the Benson Latin American Collection, and the Fine Arts Library as well as digital materials like the steaming film Miss Major! (a documentary about Miss Major Griffin-Gracy, a formerly incarcerated Black transgender elder and activist who has been fighting for the rights of trans women of color for over 40 years). The content in the collection spans fiction, science-fiction, memoir and biography, critical theory, fine art, music, poetry theater, and film.

An exhibit featuring selections from the BQSC is now on display in the Scholars Commons at the PCL.