Open Access Week is October 20-26, 2014. We are highlighting members of the LMU community, who share why open access matters to them and how they've incorporated open access into their research, instruction, and publications.
Kam Dahlquist, Associate Professor, Biology at LMU
What got you interested in Open Access?
I first became interested in Open Access when I was a postdoctoral researcher at the Gladstone Institutes/UCSF working in the field of bioinformatics. A number of scientists in this field that I knew had signed “An Open Letter to Scientific Publishers” that called for the placement of scholarly papers into a freely accessible format that could be read by anyone and that could also be computed upon. The latter aspect was important because bioinformatics scientists could then write software that would automatically extract information from published papers (called “data-mining”). This would only be possible if the papers were actually easily and freely accessible. The scientists that signed the open letter also pledged to only publish and peer review papers from Open Access journals. At the time, I chose not to sign the letter because I was not able to commit to that restriction at that early stage of my career. However, I did subsequently publish in Open Access journals. I have also become involved in the related movements for open source software, open data, and open science. I served on the board of the Open Bioinformatics Foundation and chaired the Bioinformatics Open Source Conference (BOSC) for three years (2008, 2009, 2010).
What do you see as the value of Open Access?
The value of Open Access is that it makes science accessible to everyone, not just to those who can afford to pay for journal subscriptions. This includes scientists and students at smaller institutions like LMU that do not have the budgets to pay subscription fees for all journals, but also scientists in developing nations, and the general public. Most of the biomedical research performed in the United States is funded by taxpayer dollars; it makes sense that the public should have direct and immediate access to the results of that research.
How have you incorporated Open Access in the distribution of research data and publications?
I have published in the Open Access journals Genome Biology and BMC Bioinformatics. I also edited the conference proceedings for BOSC 2010 that appeared in BMC Bioinformatics. I am currently co-directing three open source software projects: XMLPipeDB (with Dr. John David N. Dionisio in the Department of Electrical Engineering & Computer Science), GRNmap (with Dr. Ben G. Fitzpatrick in the Department of Mathematics) and GRNsight (with Dr. Dionisio and Dr. Fitzpatrick). Each of these projects has involved many LMU students over the years. I also maintain a lab wiki at OpenWetWare.org, which promotes open science.
Three of my courses also have an online wiki that is publicly accessible: Biology 367: Biological Databases (co-taught with Dr. Dionisio and cross-listed with Computer Science), Biology 368: Bioinformatics Laboratory, and Biology 398: Biomathematical Modeling (co-taught with Dr. Fitzpatrick). In the Biological Databases course, students use the open source XMLPipeDB project to create a gene database for a microorganism and then use it to analyze publicly available DNA microarray data for that organism. The gene databases that the students create are then made available to the entire scientific community. In the Bioinformatics Laboratory course, students also analyze publicly available DNA sequence, protein structure, and DNA microarray data. In Biomathematical Modeling, students use the GRNmap software to model gene regulatory networks and the GRNsight software to visualize the results. Dr. Dionsio and I also published a paper about the first incarnation of the Biological Databases course in the ACM SIGSCE journal entitled “Improving the computer science in bioinformatics through open source pedagogy”, which ironically was not Open Access, but at the time was the best venue for publishing our work. I am also in the midst of preparing a manuscript based on DNA microarray data collected in my wet laboratory; those data will be deposited into a public database upon submission of the publication for review. Thus, Open Access for publications, software, data, and coursework is incorporated into both my research and teaching.
What do you think LMU could do to play a role in the Open Access movement?
Scientific publishing is in a transitional phase right now where the publications I need to read can be found both in subscription-based journals and Open Access journals. In general, for subscription-based journals, no fee is charged to the author for publication, but a fee is charged to the reader for access to the article. In the Open Access system, a fee is charged to the author and the reader gets access to the article for free. So, during this transitional phase, there are fees being collected on both ends, which is still expensive. I would prefer to publish my papers in Open Access journals, but that means that I need to come up with the money for the publication fee. LMU could support the Open Access movement by defraying the costs for publication in Open Access journals by LMU authors. The Seaver College of Science and Engineering is currently in the process of creating guidelines for how this will be done.