Library Guides: Neuroscience: Data & Software

Data & Software

Hardware for UC Berkeley students

Student Technology Equity Program (STEP)
A program of Technology @ Berkeley, STEP provides free loaner laptops, Wi-Fi hotspots, or other peripherals such as webcams and headphones to undergraduate and graduate students based on financial need, previous support received, and instructional role (e.g., GSI). STEP accepts applications on a rolling basis throughout the academic year, while supplies last.
Laptop & equipment lending
Laptops, cables/adaptors, headphones, and other devices and equipment available to borrow. Electronic Devices Lending Policy.

Software for UC Berkeley students, faculty, and staff

Software @ Berkeley
Download site for software licensed campuswide and freely available to UC Berkeley faculty, staff and students with CalNet authentication. Includes Adobe Creative Cloud, LastPass Premium, and MS Office 365.

Collaboration, file sharing and storage

Please contact Research Data Management (researchdata@berkeley.edu) before storing or sharing human data.

bCal
Berkeley-wide calendaring system. Schedule events and meetings and set up notifications.
bDrive
Berkeley instance of Google Drive. Limited storage being phased in through April 2023.
Berkeley Box
50 GB of online file storage and sharing, available to UCB faculty, staff, and students.
bCourses Projects
2 GB storage for collaborative courses and projects.

Electronic Lab Notebooks (ELNs)

Jupyter
The Jupyter Notebook is an open source, interactive data science and scientific computing platform for research data documentation.

The following ELNs offer free trials or versions (UC Berkeley does not recommend or discourage the use of any particular ELN)

Data Management

Data Management: Guidance

Research Data Management at UC Berkeley
Learn more about RDM services at UC Berkeley.
Research Data Management Program
Consulting, training and documentation in all things data: collection, classification & security, organization, sharing, storage, backup & transfer.
Data Management General Guidance
Information on formatting, organizing, documenting, storing, sharing, preserving and citing data. [CDL]
NIH scientific data sharing policies
Information on NIH's sharing policies for scientific data, genomic sequences, research tools, model organisms, and more.
NSF data management plan requirements
Guidelines from the National Science Foundation on the data management plans required for all grant proposals. [NSF]

Data Management: Tools

DMPTool
The Data Management Planning Tool offers step-by-step templates for many different funders, including NSF, NIH, and USDA.
Dryad
An open-source, research data curation and publication platform. Berkeley is a partner and offers Dryad as a free service for all Berkeley researchers to publish and archive their data. Datasets published in Dryad receive a citation and can be versioned at any time. Dryad is integrated with hundreds of journals and is an easy way to both publish data and comply with funder and publisher mandates.
EZID
Create persistent identifiers for data, samples, and archived files.
ORCID
Open Researcher and Contributor ID enables you to register a unique and persistent personal identifier. ORCID enables links between you and your articles, presentations, and other products of scholarship.

Data Management: Repositories

Open Access Directory: Data Repositories
A list of repositories and databases for open data.
re3data: Registry of Research Data Repositories: Life Sciences
A global registry of research data repositories for the permanent storage and access of data sets to researchers, funding bodies, publishers and scholarly institutions.

Software training

Software training, workshops and consultations

Join the e-mail lists of these organizations to receive announcements about workshops, seminars, and other events.

Library workshop calendar
Drop-in workshops on citation managers, productivity software, advanced literature searching, bioinformatics tools, data visualization, R, and other topics.
Berkeley Institute for Data Science (BIDS) training programs
Software trainings, workshops, conferences, and poster sessions for data-intensive research.
California Institute for Quantitative Biosciences (QB3)
Focusses on the intersection of the physical and biological sciences and engineering. Programs include graduate and postdoc career development, undergraduate biotech internships, lab fundamentals bootcamp, and the Science Leadership and Management seminar (SLAM).
Research areas
Center for Computational Biology Workshops & Bootcamps
Bootcamps, core skills seminars, and resources for bioinformatics programming and analysis.
D-Lab Calendar
Trainings and workshops for commonly used statistical software such as R and Python. D-Lab also offers consultations and hosts working groups. Subscribe to the D-Lab newsletter for announcements of upcoming workshops.
Innovative Genomics Institute
IGI researchers deploy genome engineering to address disease, food security and environmental issues.
Research programs

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An academic partnership between UC Berkeley and UCSF.
NCBI tutorials
The NCBI section of the NLM YouTube channel features dozens of video tutorials on using NCBI tools and other resources.
NCBI webinars and courses
Both upcoming and archived/recorded webinars and online courses from NCBI.
UC Davis Genome Center
Intensive (often multi-day) workshops and trainings for genomics tools and analysis. Fees are sometimes charged (UC participants receive discounts). UC Davis can be reached via the Davis/Berkeley shuttle, BART/Amtrak, or car.
UCSF Library Events Calendar
Trainings offered by the UCSF Library. Contact instructor for permission to attend.

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Topics have included R, R Bioconductor, Python, Single Cell RNA-Seq Analysis, citation management, systematic reviews, and more.

Neuroscience data sources

Collaborative Research in Computational Neuroscience (CRCNS)
Platform for shared high quality neuroscience datasets supported by the CRCNS funding program.
International Neuroinformatics Coordinating Facility (INCF)
Nonprofit organization hosting resources including INCF Dataspace of shared neuroscience data, text, images, sounds, movies, models and simulations.
Neuroscience Information Framework (NIF)
Online public neuroscience data, materials, and tools. (NIH Blueprint for Neuroscience Research)
OpenfMRI
Freely available functional magnetic resonance imaging (fMRI) datasets
Open Microscopy Environment
Open-source software and data format standards for the storage and analysis of biological microscopy data.

For more help

Elliott Smith

he/him

Contact:

Bioscience, Natural Resources &
Public Health Library
epsmith@berkeley.edu

Subjects: Biological Sciences, Biology, Comparative Biochemistry, Integrative Biology, Molecular and Cell Biology, Neuroscience

Secondary menu

Neuroscience: Data & Software

Data & Software

Data Management

Software training

Neuroscience data sources

For more help