Text Data Mining and Publishing
Thursday, March 12, 11:10am-12:30pm
D-Lab, 350 Barrows Hall
If you are working on a computational text analysis project and have wondered how to legally acquire, use, and publish text and data, this workshop is for you! We will teach you 5 legal literacies (copyright, contracts, privacy, ethics, and special use cases) that will empower you to make well-informed decisions about compiling, using, and sharing your corpus. By the end of this workshop, and with a useful checklist in hand, you will be able to confidently design lawful text analysis projects or be well positioned to help others design such projects. Register at bit.ly/dp-berk
Upcoming Workshops in this Series 2020:
- HTML/CSS Toolkit for Digital Projects
- By Design: Graphics & Images Basics
- Publish Digital Books & Open Educational Resources with Pressbooks
Please see bit.ly/dp-berk for details.
David Eifler, the Environmental Design Librarian, will be offering a day of Zotero workshops on Thursday, September 26 in 305 Wurster Hall. The 1-hour introduction to Zotero will repeat at 9am, 11am, 2pm, 4pm, and 5pm.
Registration is not required. You are encouraged to download the program and browser connector at www.zotero.org before attending.
It’s that time of year again. Students are back on campus, classes are in session, and the Library’s Office of Scholarly Communication Services is here to help everyone hit the ground running with resources and workshops on digital publishing, copyright, and open access to research.
As usual, there’s a lot going on!
On September 25 we’re hosting a workshop on Copyright and Fair Use in Digital Projects. With pretty much everyone being a digital creator these days, the training will help you navigate copyright, fair use, and other rights related to including third-party content in your digital project. We’ll also provide an overview of what your intellectual property rights are as a creator and ways to license and share your own work too.
We’re happy to again present a series of publishing workshops to guide graduate students and postdocs on a variety of copyright, publishing, and scholarly impact issues. On October 22 we’ll be talking about copyright questions and legal considerations for your dissertation or thesis. October 23 we’re hosting a panel discussion on how to navigate the publication process from dissertation to first book. The event will include discussion from a university press acquisitions editor, a first-time book author, and an author rights expert. And October 25 we’re wrapping up the week with a workshop that will provide participants with practical strategies and tips for promoting your scholarship, increasing citations, and understanding scholarly reach and metrics.
There are lots of ways the Office of Scholarly Communication Services is here to help faculty, students, and staff. A quick rundown:
- Check out our website which has helpful information on a variety of topics, including copyright and fair use, the scholarly publishing lifecycle and sharing research data, UC’s Open Access Policy and OA funding opportunities, and much more.
- Interested in creating an open digital textbook? Take a look at UC Berkeley’s Open Book Publishing platform (anyone with a Berkeley email can signup for a free account), and get in touch with us about our Open Educational Resources (OER) grant program.
- Keep an eye on our events calendar for more workshops and trainings.
- Follow our blog and social media.
Want help or more information? Send us an email. We can provide individualized support and personal consultations, in-class and online instruction, presentations and workshops for small or large groups & classes, and customized support and training for departments and disciplines.
This nationwide campaign is designed to raise awareness about data management, security, sharing, and preservation. Students, researchers, librarians and data specialists are invited to attend these events to gain hands on experience, learn about resources, and engage in discussion around data needs throughout the research process.
To register for these events and find out more, please visit: https://guides.lib.berkeley.edu/ldw2019
MONDAY, FEBRUARY 11
Intro to Savio workshop
3:30-5:00 pm, Dwinelle 117 (Academic Innovation Studio)
Berkeley Research Computing is offering an introductory training session on using Savio, the campus Linux high-performance computing cluster. We’ll give an overview of how the cluster is set up, different ways you can get access to the cluster, logging in, transferring files, accessing software, and submitting and monitoring jobs. New, prospective, and current users are invited.
TUESDAY, FEBRUARY 12
Code Ocean lunch & learn
12:00-1:00 pm, Doe Library, Room 190 (BIDS)
Join us for a demonstration and Q&A session on the Code Ocean platform! Code Ocean is a cloud-based computational reproducibility platform that provides researchers and developers an easy way to share, discover, and run code published in academic journals and conferences.
TUESDAY, FEBRUARY 12
Preparing your data and code for reproducible publication
2:00-4:00 pm, Doe Library, Room 190 (BIDS)
This is a step-by-step, practical workshop to prepare your research code and data for computationally reproducible publication. The workshop starts with some brief introductory information about computational reproducibility, but the bulk of the workshop is guided work with code and data. We cover the basic best practices for publishing code and data.
WEDNESDAY, FEBRUARY 13
Shaping Clouds: Scaling Infrastructure for Research and Instruction at Berkeley
1:00-2:00 pm, Doe Library, Room 190 (BIDS)
There are many great resources for research and instruction across campus, but it can be difficult to determine what is available and where to find it. Join us for a showcase and community discussion about two cutting-edge cloud platforms, Analytic Environments on Demand (AEoD) and JupyterHub, and how best to provide a holistic ecosystem of these and other tools.
THURSDAY, FEBRUARY 14
Data Security: I just called to say I love you
1:00-2:00 pm, Dwinelle 117 (Academic Innovation Studio)
Learn what love the Information Security & Policy office shows campus and why a day without ISP would break the University’s heart. We will also talk about simple ways you can protect your identity and show your data love.
The Library’s Office of Scholarly Communication Services is holding a series of workshops in October focused on publishing and professional development training for graduate students and early career researchers. All workshops will take place during the week of October 22 at the Graduate Professional Development Center, 309 Sproul Hall. Light refreshments will be served.
Tuesday, October 23 | 1-2:30 p.m. | 309 Sproul Hall | RSVP
This workshop will provide you with a practical workflow for navigating copyright questions and legal considerations for your dissertation or thesis. Whether you’re just starting to write or you’re getting ready to file, you can use this workflow to figure out what you can use, what rights you have, and what it means to share your dissertation online.
Wednesday, October 24 | 1-2:30 p.m. | 309 Sproul Hall | RSVP
Hear from a panel of experts – an acquisitions editor, a first-time author, and an author rights expert – about the process of turning your dissertation into a book. You’ll come away from this panel discussion with practical advice about revising your dissertation, writing a book proposal, approaching editors, signing your first contract, and navigating the peer review and publication process.
Friday, October 26 | 1-2:30 p.m. | 309 Sproul Hall | RSVP
This workshop will provide you with practical strategies and tips for promoting your scholarship, increasing your citations, and monitoring your success. You’ll also learn how to understand metrics, use scholarly networking tools, evaluate journals and publishing options, and take advantage of funding opportunities for Open Access scholarship.
— Yasmina Anwar (@yasmina_anwar) February 13, 2018
Last week, the University Library, the Berkeley Institute for Data Science (BIDS), the Research Data Management program were delighted to host Love Data Week (LDW) 2018 at UC Berkeley. Love Data Week is a nationwide campaign designed to raise awareness about data visualization, management, sharing, and preservation. The theme of this year’s campaign was data stories to discuss how data is being used in meaningful ways to shape the world around us.
At UC Berkeley, we hosted a series of events designed to help researchers, data specialists, and librarians to better address and plan for research data needs. The events covered issues related to collecting, managing, publishing, and visualizing data. The audiences gained hands-on experience with using APIs, learned about resources that the campus provides for managing and publishing research data, and engaged in discussions around researchers’ data needs at different stages of their research process.
Participants from many campus groups (e.g., LBNL, CSS-IT) were eager to continue the stimulating conversation around data management. Check out the full program and information about the presented topics.
Photographs by Yasmin AlNoamany for the University Library and BIDS.
LDW at UC Berkeley was kicked off by a walkthrough and demos about Scopus APIs (Application Programming Interface), was led by Eric Livingston of the publishing company, Elsevier. Elsevier provides a set of APIs that allow users to access the content of journals and books published by Elsevier.
In the first part of the session, Eric provided a quick introduction to APIs and an overview about Elsevier APIs. He illustrated the purposes of different APIs that Elsevier provides such as DirectScience APIs, SciVal API, Engineering Village API, Embase APIs, and Scopus APIs. As mentioned by Eric, anyone can get free access to Elsevier APIs, and the content published by Elsevier under Open Access licenses is fully available. Eric explained that Scopus APIs allow users to access curated abstracts and citation data from all scholarly journals indexed by Scopus, Elsevier’s abstract and citation database. He detailed multiple popular Scopus APIs such as Search API, Abstract Retrieval API, Citation Count API, Citation Overview API, and Serial Title API. Eric also overviewed the amount of data that Scopus database holds.
In the second half of the workshop, Eric explained how Scopus APIs work, how to get a key to Scopus APIs, and showed different authentication methods. He walked the group through live queries, showed them how to extract data from API and how to debug queries using the advanced search. He talked about the limitations of the APIs and provided tips and tricks for working with Scopus APIs.
Eric left the attendances with actionable and workable code and scripts to pull and retrieve data from Scopus APIs.
On the second day, we hosted a Data Stories and Visualization Panel, featuring Claudia von Vacano (D-Lab), Garret S. Christensen (BIDS and BITSS), Orianna DeMasi (Computer Science and BIDS), and Rita Lucarelli (Department of Near Eastern Studies). The talks and discussions centered upon how data is being used in creative and compelling ways to tell stories, in addition to rewards and challenges of supporting groundbreaking research when the underlying research data is restricted.
Claudia von Vacano, the Director of D-Lab, discussed the Online Hate Index (OHI), a joint initiative of the Anti-Defamation League’s (ADL) Center for Technology and Society that uses crowd-sourcing and machine learning to develop scalable detection of the growing amount of hate speech within social media. In its recently-completed initial phase, the project focused on training a model based on an unbiased dataset collected from Reddit. Claudia explained the process, from identifying the problem, defining hate speech, and establishing rules for human coding, through building, training, and deploying the machine learning model. Going forward, the project team plans to improve the accuracy of the model and extend it to include other social media platforms.
Next, Garret S. Christensen, BIDS and BITSS fellow, talked about his experience with research data. He started by providing a background about his research, then discussed the challenges he faced in collecting his research data. The main research questions that Garret investigated are: How are people responding to military deaths? Do large numbers of, or high-profile, deaths affect people’s decision to enlist in the military?
Garret discussed the challenges of obtaining and working with the Department of Defense data obtained through a Freedom of Information Act request for the purpose of researching war deaths and military recruitment. Despite all the challenges that Garret faced and the time he spent on getting the data, he succeeded in putting the data together into a public repository. Now the information on deaths in the US Military from January 1, 1990 to November 11, 2010 that was obtained through Freedom of Information Act request is available on dataverse. At the end, Garret showed that how deaths and recruits have a negative relationship.
Orianna DeMasi, a graduate student of Computer Science and BIDS Fellow, shared her story of working with human subjects data. The focus of Orianna’s research is on building tools to improve mental healthcare. Orianna framed her story about collecting and working with human subject data as a fairy tale story. She indicated that working with human data makes security and privacy essential. She has learned that it’s easy to get blocked “waiting for data” rather than advancing the project in parallel to collecting or accessing data. At the end, Orianna advised the attendees that “we need to keep our eyes on the big problems and data is only the start.”
Rita Lucarelli, Department of Near Eastern Studies discussed the Book of the Dead in 3D project, which shows how photogrammetry can help visualization and study of different sets of data within their own physical context. According to Rita, the “Book of the Dead in 3D” project aims in particular to create a database of “annotated” models of the ancient Egyptian coffins of the Hearst Museum, which is radically changing the scholarly approach and study of these inscribed objects, at the same time posing a challenge in relation to data sharing and the publication of the artifacts. Rita indicated that metadata is growing and digital data and digitization are challenging.
It was fascinating to hear about Egyptology and how to visualize 3D ancient objects!
We closed out LDW 2018 at UC Berkeley with a session about Research Data Management Planning and Publishing. In the session, Daniella Lowenberg (University of California Curation Center) started by discussing the reasons to manage, publish, and share research data on both practical and theoretical levels.
Daniella shared practical tips about why, where, and how to manage research data and prepare it for publishing. She discussed relevant data repositories that UC Berkeley and other entities offer. Daniela also illustrated how to make data reusable, and highlighted the importance of citing research data and how this maximizes the benefit of research.
At the end, Daniella presented a live demo on using Dash for publishing research data and encouraged UC Berkeley workshop participants to contact her with any question about data publishing. In a lively debate, researchers shared their experiences with Daniella about working with managing research data and highlighted what has worked and what has proved difficult.
We have received overwhelmingly positive feedback from the attendees. Attendees also expressed their interest in having similar workshops to understand the broader perspectives and skills needed to help researchers manage their data.
I would like to thank BIDS and the University Library for sponsoring the events.
For an office that does not offer catalog-listed courses, the Oral History Center is still deeply invested in — and engaged with — the teaching mission of the university.
For over 15 years, our signature educational program has been our annual Advanced Oral History Summer Institute. Started by OHC interviewer emeritus Lisa Rubens in 2002 and now headed up by staff historian Shanna Farrell, this week-long seminar attracts about 40 scholars every year. Past attendees have come from most states in the union and internationally too — from Ireland and South Korea, Argentina and Japan, Australia and Finland. The Summer Institute, applications for which are now being accepted, follows the life cycle of the interview, with individual days devoted to topics such as “Project Planning” and “Analysis and Interpretation.”
In 2015 we launched the Introduction to Oral History Workshop, which was created with the novice oral historian in mind, or individuals who simply wanted to learn a bit more about the methodology but didn’t necessarily have a big project to undertake. Since then, a diverse group of undergraduate students, attorneys, authors, psychologists, genealogists, park rangers, and more have attended the annual workshop. This year’s workshop will be held on Saturday February 3rd and registration is now open.
In addition to these formal, regularly scheduled events, OHC historians and staff often speak to community organizations, local historical societies, student groups, and undergraduate and graduate research seminars. If you’d like to learn more about what we do at the Center and about oral history in general, please drop us a note!
In recent years we have had the opportunity to work closely with a small group of Berkeley undergrads: our student employees. Although the Center has employed students for many decades, only in the past few years have they come to play such an integral role in and make such important contributions to our core activities. Students assist with the production of transcripts, including entering narrator corrections and writing tables of contents; they work alongside David Dunham, our lead technologist, in creating metadata for interviews and editing oral history audio and video; and they partner with interviewers to conduct background research into our narrators and the topics we interview them about. With these contributions, students have helped the Center in very real, measurable ways, most importantly by enabling an increase in productivity: the past few years have been some of the most productive in terms of hours of interviews conducted in the Center’s history. We also like to think that by providing students with intellectually challenging, real-world assignments, we are contributing to their overall educational experience too.
As 2017 draws to a close, I join my Oral History Center colleagues Paul Burnett, David Dunham, Shanna Farrell, and Todd Holmes in thanking our amazing student employees: Aamna Haq, Carla Palassian, Hailie O’Bryan, Maggie Deng (who wrote her first contribution to our newsletter this issue), Nidah Khalid, Pilar Montenegro, Vincent Tran, and Marisa Uribe!
Martin Meeker, Charles B. Faulhaber Director of the Oral History Center
CFP deadline December 1, 2017.
A one-week training workshop (March 25-31, 2018) at UCSC on photogrammetry for early-stage graduate students. Participants in this workshop will gain intensive hands-on experience in the techniques and processing workflow for photogrammetric recording for cultural heritage projects, presented within the context of a critical engagement in discussions of the politics of digital knowledge production. Click here for more information: ARC Photogrammetry Workshop Call UCSC.
CFP deadline January 19, 2018.
Scholars from a wide range of fields are invited to submit proposals for research projects investigating Ed Ruscha’s “Streets of Los Angeles” archive—including, but not limited to digital humanities, cultural geography, architecture, art history, photography, and visual culture. Interdisciplinary approaches and team-based projects are particularly encouraged. Selected researchers would collaborate with Getty Research Institute (GRI) staff as part of a larger research-technology project, which seeks to digitize and make publicly-accessible a portion of the archive in innovative ways. The goal is to publish resulting scholarship at the close of the project. For more details, click here.
CFP deadline Janurary 5, 2018.
This Getty Foundation supported workshop will support interdisciplinary teams focused on the hard questions of Digital Art History as a discipline, a set of methods, and a host of technical and institutional challenges and opportunities.
Participants will gather from June 4-16, 2018 in Venice, Italy at Venice International University, with follow-up activities taking place over the course of the 2018-19 academic year, and leading into a follow-on gathering in Summer of 2019 that will operate as a writing and digital publication workshop, building upon work done over the course of the year by the project teams and in collaboration with our wider network.
CFP deadline January 16, 2018.
Digital Humanities Advancement Grants (DHAG) support digital projects throughout their lifecycles, from early start-up phases through implementation and long-term sustainability. Experimentation, reuse, and extensibility are hallmarks of this grant category, leading to innovative work that can scale to enhance research, teaching, and public programming in the humanities.
This program is offered twice per year. Proposals are welcome for digital initiatives in any area of the humanities.
Friday, Dec. 8
Open Textbook Workshop – Faculty & Lecturers
9:30-11:30 a.m. | Academic Innovation Studio, 117 Dwinelle Hall
Are you an instructor who is concerned about the impact of high textbook costs on your students? Are you considering adopting or creating innovative pedagogical materials? Explore possible open textbook solutions by attending a two hour workshop and writing a short textbook review. The Library will provide you with a $200 stipend for your efforts! Space is limited, so please submit a very brief application form:
Friday, Dec. 8
Open Textbook Workshop – Staff & Campus Partners
12:45 p.m. – 2:45 p.m. | Academic Innovation Studio, 117 Dwinelle Hall
Are you a UC Berkeley staff or affiliate who is concerned about the impact of high textbook costs on students, or you are working with a faculty member who is? Do you want to support the adoption or creation of innovative pedagogical materials? Learn the landscape, opportunities, and challenges for open textbooks, and how to discuss whether open textbooks are a good fit.
Tuesday, Feb. 20
Publish Digital Books and Open Textbooks with Pressbooks
1:10-2:30 p.m. | Academic Innovation Studio, Dwinelle Hall 117 (Level D)
If you’re looking to self-publish work of any length and want an easy-to-use tool that offers a high degree of customization, allows flexibility with publishing formats (EPUB, MOBI, PDF), and provides web-hosting options, Pressbooks may be great for you. Pressbooks is often the tool of choice for academics creating digital books, open textbooks, and open educational resources, since you can license your materials for reuse however you desire. Learn why and how to use Pressbooks for publishing your original books or course materials. You’ll leave the workshop with a project already under way!
A representative from Qiagen will offer a hands-on training workshop on using IPA to interpret expression data (including RNA-seq).
You are invited to participate in this free training, and are encouraged to bring your own laptop or use the computer workstations in our training room.
Please register if you are interested in attending.
The workshop will cover how to:
- Format, upload your data, and launch an analysis
- Identify likely pathways that are expressed
- Find causal regulators and their directional effect on gene functions and diseases
- Build pathways, make connections between entities, and overlay multiple datasets on a pathway or network
- Understand the affected biological processes
- Perform a comparison analysis: utilize a heat map to easily visualize trends across multiple time points or samples
Questions? Please contact Elliott Smith (firstname.lastname@example.org)