Open Access Week Activities at UC Berkeley

October 19-23 is Open Access Week. In honor of this week, there will be on-campus events celebrating this growing movement! Below is a list of activities happening on campus this week. Please go here, to see the original announcement.

• E-Scholarship (CDL) for UCB Anthropology/Archaeology: Take Control of Your Publications with eScholarship (4:30pm Monday)
• The Future of Open Access (4pm Tuesday)
• Live Webinar from the Open Access Scholarly Publishing Association (OASPA) on the promise and perils of OA publishing. (9am Pacific time Tuesday, in the Bioscience and Natural Resources Library Seminar Room, 2101 Valley Life Sciences Building)
• Academic Writing and Publishing 2.0: eJournals, Blogs, Wikis, Tweets (noon Wednesday)

And a related event:

• Article-level Metrics at PLoS: What are they and why should you care? (noon Monday November 9)

Take Control of Your Publications with eScholarship

An Open Access Week presentation open to all Anthropology faculty and graduate students, ARF affiliates, and other interested students and faculty

Catherine Mitchell

Director, CDL Publishing Group

University of California

Monday, October 19, 2009

4:30 – 6.00 p.m.

Archaeological Research Facility, 2251 College Building, Room 101

• Keep your copyright

• Reach more readers

• Publish when you want to

• Protect your work’s future

…all with no fees

eScholarship offers a robust open access* publishing platform that enables departments, research units, publishing programs, and individual scholars associated with the University of California to have direct control over the creation and dissemination of the full range of their scholarship, including:

• Journals • Conference Proceedings

• Books • Working Papers

• Postprints • Seminar/Paper Series

Initiated in 2002, eScholarship  is an intiative of the California Digital Library. It now houses over 30,000 publications with more than 9 million full-text downloads to date. The rate of usage of these materials has grown dramatically in the past 7 years, now often exceeding 170,000 downloads per month.

http://www.cdlib.org/programs/escholarship.html

Come learn how you can get started publishing with eScholarship today!

“Open-access (OA) literature is digital, online, free of charge, and free of most copyright and licensing restrictions…OA is entirely compatible with peer review, and all the major OA initiatives for scientific and scholarly literature insist on its importance.”

Source:  Peter Suber:  http://www.openaccessweek.org/wp-content/uploads/a-very-brief-intro-a4.pdf

UC Berkeley joins five-member open access pact; BRII extended for another year

UC Berkeley, along with Cornell, Dartmouth, Harvard, and the Massachusetts Institute of Technology have formed a five-member pact, in order to “provid[e] ‘barrier-free access to information’ — from DNA-sequencing data to medical research to sociological studies — to academics and the general public alike.” In order to fulfill its promise in the pact, the Berkeley Research Impact Initiative (BRII), which was launched as a pilot program in January 2008, will be extended for another year.  BRII “subsidize[s] scholars who choose to make their work available online at no cost to readers.” Click here to see October 2 article from Berkeleyan.

OKAPI Island News

Over the past two years, OKAPI Island in Second Life has supported the research, teaching, and learning of dozens of scholars. OKAPI Island has also hosted numerous public programs and outreach activities. This post highlights key accomplishments and updates.

Awards
2007 Open Archaeology Prize
2008 NMC Virtual Learning Award

Public Programs
Burning Catalhoyuk Day. December 10, 2008
Presidio Teacher Night. October 1, 2008
iSummit Keynote Webcasts. July 30-31, 2008
Cal Day. April 8, 2008
Remixing Catalhoyuk Day. November 28, 2007

Second Life DeCal Courses
http://www.decal.org/784 (Fall 2008)
http://www.decal.org/930 (Spring 2009)

Anthropology 39B: Serious Games for Archaeology and Imagining the Past (Fall 2009)
http://anthropology.berkeley.edu/programs/courses/course_details.php?id=313

Undergraduate Research Apprentice Program (offered for the fourth consecutive semester)
Sharing a Sense of Place: Constructing a Neolithic Village in Second Life
http://research.berkeley.edu/urap/projects/detail.lasso?-Search=Action&-Table=pub_details&-Database=urap_web&-KeyValue=508

Interview: “Second Life as an Archaeological Tool”
An Interview with Berkeley Archaeology Professor Ruth Tringham
National Center for Preservation Technology and Training. June 18, 2009.
http://www.ncptt.nps.gov/second-life-as-an-archaeological-tool/

Journal Article
Morgan, Colleen. “(Re)Building Çatalhöyük: Changing Virtual Reality in Archaeology” Archaeologies. July 2009.
http://www.springerlink.com/content/k254u1q4tt357918

More Info
http://okapi.wordpress.com/projects/okapi-island-in-second-life/

Machinima
“Basket Weaving at Catalhoyuk” by Colleen Morgan
more:  http://middlesavagery.wordpress.com/2009/04/15/basket-weaving-at-catalhoyuk/

Ars Synthetica Prototype Launches

http://www.ars-synthetica.net

We are pleased to announce the launch of a working prototype (beta release) of Ars Synthetica, a web-based multimedia forum for engaging specialists and non-specialists in an informed, ethical, and democratic dialogue on the emerging field of synthetic biology.

Anthropology professor Paul Rabinow introduces Ars Synthetica to his colleagues.

Ars Synthetica is a collaboration between Open Knowledge and the Public Interest, the Anthropology of the Contemporary Research Collaboratory, and the Synthetic Biology Engineering Research Center (Harvard, Berkeley, MIT, QB3, UCSF, Prairie View A&M). The site is designed to provide multiple participatory channels for exploring questions about ethics, security, and how cutting-edge research in the biosciences is organized, governed, funded, and expanded. How will synthetic biology shape and be shaped by medicine, energy, and environmental needs? Whose business is ethics? What are the limits to what we can design? These are the kinds of questions that Ars Synthetica poses to expert and lay communities alike. Our goal is to actively resist the polemics that often characterize public discourse about new science and technology. We seek the fertile grounds for discourse between the hype of revolution on the one side and fears of “playing God” on the other. The outcome will not provide absolute or final answers, but  enable a diverse range of participant responses, perspectives, and concerns.

Ars Synthetica will feature many student projects, such as this multimedia piece by Marlee Tichenor

We are releasing the site  as a public beta, while the Ars Synthetica team develops site content, expands participation and gathers feedback before the next round of development. During the Spring ‘09 semester, students in Professor Rabinow’s graduate and undergraduate courses will be preparing content for Ars Synthetica.

Features of Ars Synthetica:

Pathways
Provide a means of representing and giving form to nonlinear connections among the many elements of the Ars Synthetica site. We anticipate developing and allowing our community to develop multiple nonlinear pathways through Ars Synthetica.

Problems, Truth Claims & Debates
Ars Synthetica features Problems, Truth Claims and Debates, designed to engage visitors in reflection and dialogue around emerging issues in the life sciences.  Whose business is ethics? Are there limits to what we can design? Are biologists playing God? Ars Synthetica users can contribute to existing  Problems, Truth Claims and Debates or contribute new ones.

Archive
The Archive contains abstracts and full publications related to synthetic biology, including scientific journal articles and popular press publications.

Contribute
Allows visitors to upload their own multimedia products, including  research papers and multimedia works. Once uploaded, others can comment on the works of others.

Blog
The blog aggregates posts from multiple authors and blogs, including On the Assembly of Things, Vital Systems Security, Biopower and the Contemporary, and Synbio and the Technocrat, and the student-run iGEM blog.

Platform
The Website is built using Omeka, open-source software for museum exhibits and collections. The site uses a custom version of our OKAPI exhibit template for Omeka.

Web 2.0
The site is distributed  across the web, leveraging multiple technologies and services, including  MediaWiki, YouTube, Blip.tv, Flickr, Scribd, and Vuvox.

Ars Synthetica: Designs for Human Practice
Explore this publication, authored by Paul Rabinow and Gaymon Bennett, to learn more about the ideas underlying this project.

Public Understanding of Research Program
This project was developed under OKAPI’s Public Understanding of Research Program.

Welcome President Obama!

Sproul Plaza, University of California, Berkeley, January 20, 2009

OKAPI welcomes a new era of transparency and accountability in government.  The recently-launched whitehouse.gov will prioritize communication, transparency and participation.

OKAPI Releases Theme for Museum Collection Software

Open Knowledge and the Public Interest (OKAPI) is pleased to announce the release of the Okapi theme package for Omeka, a web-based platform for publishing museum exhibits and collections developed by the Center for History and New Media at George Mason University. The Okapi theme package enables Omeka users without expert web design skills to create polished multimedia exhibits and collections. The home page features a cinematic 980×500 pixel main image and up to four featured exhibits.  Exhibit pages include new layouts for articles, themed collections and embedded multimedia.  The bundled Multimedia Links plugin enables embedding of html code, flash video (flv), and many other formats supported by the included JWplayer. The theme displays accessible Flash-based typography and is W3C CSS and XHTML compliant. The Okapi theme package (Okapi theme, Multimedia Links plugin and exhibit layouts) were developed by independent developer Kristin “Chach” Sikes in collaboration with Open Knowledge and the Public Interest. The Okapi theme package is available for download from the Omeka Website and is released under a General Public License (GPL).

The OKAPI theme package includes the following:

Okapi Theme (Default Settings)
Home Page: Displays cinematic (980×500 pixel) main image, and up to four thumbnail images of featured resources Header/Navigation: Title and subtitle displayed at top of page using accessible rich typography. Semitransparent navigation tabs appear over adjustable header images on all pages. Up to four exhibits are featured on navigation. An “Exhibits” tab appears if your site includes more than four exhibits. Style Sheet: Extra style sheet (custom_style.css) enables sitewide modification of fonts and colors
Informational Pages: Themed  templates for About, Overview and Credits pages
Themed Geolocation plugins for Google Maps integration Themed Contribution plugin for user contributions Themed Items, Collections, and Exhibit pages (see Exhibit Layouts) Drag-n-Drop Media Publishing:  This theme extends Omekaʼs drag-n-drop functionality, allowing you to drag media from the archive into your exhibits layouts. Footer:  Space for links (Overview, Abouts, Credits), licensing (e.g., Creative Commons Licensing) and sponsors.

Exhibit Layouts
The Okapi Exhibit theme integrates exhibit pages with OKAPI theme and Multimedia Links plugin. The theme eliminates the section menu and allows users to publish on the Exhibit page thumbnails images and links to each section. The Okapi Exhibit theme includes four layouts:
Super Page: Allows users to theme exhibit home page and create thumbnail images for each section of exhibit.
Featured Article: Publish images and multimedia alongside feature article
Themed Collection: Publish video and a selection of up to 20 assets alongside article
Embedded HTML media:  Publish flash, widgets or other html embed code
Archive Multimedia:  Publish multimedia assets from archive using JWplayer.

Multimedia Links Plugin
Creates new Item fields for embedding html code, Flash video (flv), and many other media formats supported by the bundled JWplayer.

Media Player Integration
The open source JWplayer comes bundled with the OKAPI theme. The JWplayer supports playback of any format the Adobe Flash Player can handle (FLV, MP4, MP3, AAC, JPG, PNG and GIF). It also supports RTMP, HTTP and live streaming, various playlists and captioning formats, a wide range of settings and an extensive javascript
API. The skinning functionality allows you to completely customize its looks. Learn more here:  http://code.jeroenwijering.com/trac/

Rich Typography Support
The Okapi theme enables rich typography through accessible implementation of SIFR 3 (using Flash, JavaScript and CSS).  Learn more here:  http://wiki.novemberborn.net/sifr3

Considerations for Web Developers
CSS: The markup and CSS for this theme are loosely based on Tripoli, a CSS method that allows you to adjust your site layout relatively quickly, in multiple browsers. This is similar to Google Blueprint and Yahoo Grids, but a little lighter weight. The Tripoli method does work with liquid layouts, though this site is currently fixed-width.

SIFR3: Typography can be changed by modifying flash files and a little bit of code, documentation included.

ShadedBorders: This Javascript corner-rounding script is enabled by default, and can be used on other page elements to create a different look for your site.

OKAPI Wins Open Archaeology Prize

Alexandria Archive Institute Press Release, November 30, 2007:

Scholars from UC Berkeley swept the Open Archaeology Prize competition, held at the 2007 meeting of the American Schools of Oriental Research (ASOR). One of a series of awards around “open archaeology” funded primarily by the William and Flora Hewlett Foundation, this particular Open Archaeology Prize targeted members of ASOR, a long-standing organization of archaeologists conducting research in the Near East. The winners, who were selected based on their project’s scholarly merit, potential for reuse in research or teaching and availability on the web in a free and reusable format, were announced last week at ASOR’s annual meeting in San Diego.

First Prize, Senior Scholar
First prize for a Senior Scholar was awarded to the team led by Ruth Tringham (Professor, Department of Anthropology) and Noah Wittman (Program Manager, Open Knowledge and the Public Interest) for their website “Remixing Çatalhöyük” (http://okapi.berkeley.edu/remixing). Remixing Çatalhöyük has been variously described as a database narrative and as a multimedia exhibition and research archive. Launched in October 2007, it features the investigations and data of the Berkeley Archaeologists at Çatalhöyük (BACH) and their colleagues at the Neolithic tell settlement of Çatalhöyük, Turkey. The aim of the website, accessible in English or Turkish, is to engage the public of all ages in the exploration of primary research data through four themed collections that are selected from the research database. One theme on the Life-History of People, Places, and Things – also includes a K-12 activity module. The public are invited to download media items that are licensed with a Creative Commons 3.0 license, create original projects and contribute their own “remixes” about Çatalhöyük. Tringham and Wittman write that the developers of this resource “hope that this project will inspire other researchers to openly share their research data and engage broad public audiences.” Remixing Çatalhöyük represents a groundbreaking effort toward sharing and elucidating the past, and we certainly hope other projects will follow their lead.

First Prize, Junior Scholar
First prize for a Junior Scholar was awarded to Catherine Foster (PhD student, Department of Near Eastern Studies) for her project “Household Archaeology and the Uruk Phenomenon: A Case Study from Kenan Tepe, Turkey” (http://nes.berkeley.edu/~cpfoster/). Catherine is awarded first place for developing a website on her research involving household studies of a Late Chalcolithic community in the Upper Tigris region of southeast Anatolia. Foster explains that the ultimate goal of this project is to create an open access micro-artifact database that can be used as a reference resource for other scholars wishing to embark on this type of analysis. Because it will be open access, other scholars will be able to add to the database with high-resolution scans and descriptions or alter categories as developments are made. She states, “To my knowledge, no such database is freely available over the Internet and will be a valuable resource as the inclusion of microarchaeological techniques in Near Eastern excavation projects becomes more and more commonplace.” Foster’s project demonstrates a solid foundation in open access and a visionary approach for future sharing of research in archaeology.

Runner Up
A second prize of $200 in books, co-sponsored by the David Brown Book Company, was awarded to Justin Lev-Tov (Statistical Research, Inc.) for his project “Hazor: Zooarchaeology” (http://www.opencontext.org/database/project.php?item=HazorZooPRJ0000000010). This project presents zooarchaeological identification and analysis of nearly 10,000 animal bones from Late Bronze Age and Iron Age contexts at Hazor, research Justin conducted as part of the Hazor Excavations in memory of Yigael Yadin. By sharing this dataset in Open Context with a flexible license for reuse, Justin is improving access to high-quality research and original data that accompany published syntheses. This dataset has been accessed over 11,000 times since it was uploaded to Open Context in Fall 2006. We hope to see more related content from this time period available in open access formats so that Justin’s dataset becomes even more valuable through comparison with other sites.

The ASOR Open Archaeology Prize competition is sponsored by the Alexandria Archive Institute, promoting the development and use of open educational resources in archaeology and related disciplines. The competition aims to enhance community recognition of open scholarly communication and receives generous support from the William and Flora Hewlett Foundation, the David Brown Book Company and the American Schools of Oriental Research.

Remixing Çatalhöyük Launches

Remixing Çatalhöyük
http://okapi.berkeley.edu/remixing
The OKAPI team is pleased to announce the launch of Remixing Çatalhöyük, a multimedia exhibition and research archive featuring the investigations and discoveries of the Berkeley Archaeologists at Çatalhöyük and their colleagues. Located in central Turkey, Çatalhöyük (“cha-tal-hu-yuk”) is the site of a Neolithic farming community that flourished from 9,400 until 7,700 years ago. We invite the public to explore themed collections, create original projects, and contribute their own “remixes” of Çatalhöyük.

Remixing Çatalhöyük was constructed during the Spring 2007 semester by a team of UC Berkeley students, staff, and faculty, working in close collaboration with the Berkeley Archaeologists at Çatalhöyük (BACH). Remixing Çatalhöyük highlights and supports a multi-vocal approach to history, where the global, online community is invited to participate in the dialogue alongside the physical, local community. The OKAPI and BACH teams hope that this project will inspire other researchers to openly share their research data and engage broad public audiences.

Web Site Design
Remixing Çatalhöyük features a tripartite design, including a research archive, themed collections and an interactive web exhibition.

The Research Archive includes more than 65,000 photos, videos, articles and other multimedia research materials–all freely available under Creative Commons NonCommercial Attribution licensing.

The Remixing team curated and adapted research materials into four Themed Collections designed to engage public in the process of archaeology and support a wide range of “k to grey” teaching and learning scenarios:
• Life Histories of People, Places and Things
• Senses of Place
• Archaeology at Different Scales
• The Public Face of Archaeology
The themed collections feature intro articles, intro videos, K-12 activities, and 200 carefully selected and annotated multimedia resources from the research archive.

The Web Exhibition was designed to spark interest and provide context for numerous research materials. The interactive Site Plan (at right) allows users to zoom in and roll-over excavation site features. The Timeline (at right), Map and People gallery orient visitors and highlight the project’s multi-vocal, multi-scalar approach to archaeology.

K-12 Activity
In this unique activity co-developed by a team of archaeologists, teachers, and curriculum developers, students use archaeological evidence and their own imaginations to reconstruct life in a Neolithic household, more than 9,000 years ago. The activity is designed for middle school students and can easily be adapted for other ages. This activity complies with Section 6.1 of the California History-Social Science Content Standards for sixth grade students, which requires that “Students describe what is known through archaeological studies of the early physical and cultural development of humankind from the Paleolithic era to the agricultural revolution.”

On Remixing
Remixing Çatalhöyük is designed to advance the discovery of new ideas by facilitating the reuse of resources and ideas developed by the Berkeley Archaeologists at Çatalhöyük. The site features student projects, faculty presentations, multimedia websites, and other “remixes” of Çatalhöyük research data. We hope these examples inspire others to remix and reuse research data from this and other projects.

Archaeoblender
http://www.archaeoblender.com
Visitors are encouraged to download, remix materials, and share their remixes using Archaeoblender. Archaeoblender was developed by the OKAPI team using ccHost, an open-source application developed by the Creative Commons for sharing and remixing multimedia content.

OKAPI Island
Virtual Residents of Second Life –a multi-user online environment—can visit Okapi Island to explore 3D representations of Catalhoyuk as it exists today and as it may have looked in the past. During the Fall 2007 semester, a dozen students, faculty and staff will be completing construction of Okapi Island and preparing for a public program.

Okapi Island, location of Çatalhöyük in Second Life. Come Visit! http://slurl.com/secondlife/Okapi/128/128/0

Okapi Island Project Wiki (Join Us!)
http://okapiisland.pbwiki.com/

Accessibility
We provided a text version of the site to improve accessibility for users with low speed connections, screen readers, iPhones or other special needs.

Multilingual
The entire site (with the exception of the research database) was translated into Turkish by UC Berkeley Anthropology graduate student Burcu Tung and proofed by Stanford Anthropology graduate student Elif Babul. Tesekkür.

Dissemination
To maximize visibility and reuse, we have (or will soon) republished materials from Remixing Catalhoyuk in multiple locations, including Flickr, YouTube, Apple Learning Interchange, Connexions, Internet Archive, Wikiversity, WikiEducator, and CyArk. A future report will document the quantity and nature of traffic we receive from each site.

On Building Themed Collections
The design of our themed collections was greatly influenced by the process, products and findings of the Calisphere Themed Collections project as documented in “Handful of Things” article by Mankita et al in May 2006 issue of D-Lib Magazine.

Tips, Tools, and Templates
We paid special attention to documenting our process so that others could reuse our tools and techniques. This information is available in the Tips, Tools, and Templates section of the site.

Credits
Project Sponsors:
Paul Grey, Principal Investigator, Scholar’s Box; Professor of Engineering, UC Berkeley
David Greenbaum, Project Director, Scholar’s Box; Director of Data Services, UC BerkeleyRuth Tringham, Principal Investigator, Berkeley Archaeologists at Catalhoyuk
Michael Ashley, Manager, New Programs, Office of the CIO, UC Berkeley

“Remixing” Team:
Noah Wittman, Project Director, Remixing Çatalhöyük
Ruth Tringham, Content Direction, Pilot Instructor; Professor of Anthropology, UC Berkeley; Principal Investigator, Berkeley Archaeologists at Çatalhöyük (BACH) Project
Burcu Tung, Content Developer and Turkish Translations, Ph.D. Candidate, Department of Anthropology, UC Berkeley
Elizabeth Ha, Media Manager, Video Production
Adrian Van Allen, Web & Interaction Designer
Ruth Tepper Brown, EditorOna Johnson, Curriculum Developer
Denise Phelps, Digital Media Specialist
Michael Ashley, Information Architect
Marc Moglen, Second Life Audio Producer
Daniel Wei, Second Life Scripting and Modeling
Elif Babul, Turkish Proofing
Joseph Coburn, Interactive Designer, Demonstration Tool
Rockman et al, Evaluators

Special thanks to the Berkeley Archaeologists at Çatalhöyük and colleagues for sharing their content and expertise.

This project was made possible with funding from the US Department of Education’s Fund for the Improvement of Post-Secondary Education (FIPSE Grant #P116B040739). Additional support was provided by the Gilbert Fund, UC Berkeley’s Office of the CIO, Open Knowledge and the Public Interest, Multimedia Authoring Center for Teaching Anthropology, and the Archaeological Research Facility.

Experience from Catalhoyuk 2007: CatDV to Portfolio

In July 2007, during our season of Remediated Places project at Çatalhöyük, Steve Mills and I decided for a number of reasons to create an Extensis Portfolio catalog for the assets of the project. I had already created a catalog for the video assets using SquareBox CatDV, which is a great tool for indexing and creating videoclips and taking them straight into Final Cut Pro editing. But there are disadvantages. Steve couldn’t see or contribute to the clips because he did not own a Windows version of CatDV and moreover, we didn’t have the funds to purchase the client/server version which would be essential for our transatlantic post-season collaboration. Finally there are some disadvantages of CatDV that I mention below in regard to user fields that I find annoying, compared to the versatility of Extensis Portfiolio.

Meanwhile, Michael Ashley and the Media Vault Project are going great guns developing the use of the cross-platform client/server basis of Extensis Portfolio at UC Berkeley. Steve’s audio files had been kept in an MS Excel spreadsheet format and he was eager to have the information in a database along with the audio files themselves.

So we decided to create a catalog linked to both audio and video files of our merged assets. An alternative would have been Filemaker Pro which also enables this kind of linking. However, we chose Portfolio because of our hoped-for collaboration with the Media Vault Project since our project is embedded in the Çatalhöyük project which has been chosen as one of the MVP’s pilot projects.
We have posted the path by which we travelled technically from CatDV to Portfolio in a posting on the Remediated Places blog