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XKCD - simple writer

Only allows you to use the most common 1000 words in the English language.  

Educational use here - Introducing Students to the Challenges of Communicating Science by Using a Tool That Employs Only the 1,000 Most Commonly Used Words

 

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Sam S Donovan onto HITS 2018 Workshop Resources

Data Management Skill Building Hub

The Data Management Skillbuilding Hub contains resources for better data management and is open to community input and update. These resources are adaptable across a range of contexts and intended for use by researchers, teachers, librarians, or anyone who wants to learn better data management practices. Each tile below contains a lesson in slide format with annotations, a one page handout that distills the main message, and a hands-on exercise. 

Also see the data life cycle at DataONE.

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4) You can get your whole genome sequenced but should you? Wired article 6/26/2017

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Whole Genome Sequencing and You (10 min)

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How to Sequence the Human Genome 5min

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Allen Cell Drug Perturbation website

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Lessons from HeLa Cells:The Ethics and Policy of Biospecimens

Human biospecimens have played a crucial role in scientific and medical advances. Although the ethical and policy issues associated with biospecimen research have long been the subject of scholarly debate, the story of attention of a much broader audience. The story has been a catalyst for policy change, including major regulatory changes proposed in the United States surrounding informed consent. These proposals are premised in part on public opinion data, necessitating a closer look at what such data tell us. The development of biospecimen policy should be informed by many considerations—one of which is public input, robustly gathered, on acceptable approaches that optimize shared interests, including access for all to the benefits of research. There is a need for consent approaches that are guided by realistic aspirations and a balanced view of autonomy within an expanded ethical framework.

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Data for Democracy - Code of Ethics

Data for Democracy is partnering with Bloomberg and BrightHive to develop a code of ethics for data scientists. This code will aim to define values and priorities for overall ethical behavior, in order to guide a data scientist in being a thoughtful, responsible agent of change. The code of ethics is being developed through a community-driven approach.

By hosting discussions among data scientists, we hope to better capture the diverse interests, needs, and concerns that are at play in the community, and put together a code that is truly created by data scientists, for data scientists.

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Community Principles on Ethical Data Practices

This code of ethics for data sharing is created and proposed for adoption by the data science community to reflect the behaviors and principles for the responsible and ethical use and sharing of data by data scientists. 

As a community-driven crowdsourced effort, you can join the the discussion and contribute to the next version of the Community Principles on Ethical Data Sharing.

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Qiime2 View

This interface can view .qza and .qzv files directly in your browser without uploading to a server.

QIIME 2 View (or q2view for short) is an entirely client-side interface for viewing QIIME 2 artifacts and visualizations (.qza/.qzv files respectively). This means that you do not need to have a working QIIME 2 installation to inspect QIIME 2 results. It also means that the files you provide are not sent beyond your browser. In other words, this entire site functions without a server (which makes it very inexpensive to operate).

Additionally, q2view supports viewing externally hosted files, which means you can provide a link to your file (for example on Dropbox) and q2view will automatically download and display it. Better yet, the resulting pages are themselves shareable, so if a collaborator does not have QIIME 2, you can simply upload your results and share your q2view links with your collaborator. q2view will automatically fetch your results and display them to your collaborator.

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Allen Institute Data

The Allen Cell Explorer is the data portal for the Allen Institute for Cell Science, where you can explore our publicly available data, tools and models. The portal provides an unprecedented view into the organizational diversity of human stem cells by combining large-scale 3D imaging data, predictive models, observations of cells, detailed methods, and cell lines that can be purchased for use in labs around the world.

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Sam S Donovan onto Data Sources

Pacific Biosciences datasets

Here are some sample datasets so that you can explore PacBio® sequence data as well as file types generated by the PacBio RS and SMRT® Analysis.

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Sam S Donovan onto Data Sources

NIBLSE Core Competencies

The bioinformatics competencies that NIBLSE recommends undergraduate life sciences students have by the time they graduate. As discussed in the narrative, they are informed by the results of the national NIBLSE survey, analysis of ninety syllabi with bioinformatics content, and the cumulative expertise and experience of the authors. Following each competency is a list of three representative examples illustrating the competency. 

 

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A Primer for Computational Biology by Scott O'Neil

This is an Open Educational Resource written on the PressBooks platform. This textbook has great resources and concise chapters you can assign to students.

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Illumina presentation HITS 2018

Illumina presentation by Matt Angel on 6/12/2018.

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Data Carpentry

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Our mission is to provide researchers high-quality, domain-specific training covering the full lifecycle of data-driven research. Data Carpentry is a sibling organization of Software Carpentry. Where Software Carpentry teaches best practices in software development, our focus is on the introductory computational skills needed for data management and analysis in all domains of research. Our lessons are domain specific, from life and physical sciences to social science and build on the existing knowledge of learners to enable them to quickly apply skills learned to their own research. Our initial target audience is learners who have little to no prior computational experience. We create a friendly environment for learning to empower researchers and enable data driven discovery.

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Software Carpentry

Since 1998, Software Carpentry has been teaching researchers the computing skills they need to get more done in less time and with less pain. Our volunteer instructors have run hundreds of events for more than 34,000 researchers since 2012. All of our lesson materials are freely reusable under the Creative Commons - Attribution license.

The Software Carpentry Foundation and its sibling project, Data Carpentry, have merged to become The Carpentries, a fiscally sponsored project of Community Initiatives, a 501(c)3 non-profit incorporated in the United States.

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Science in the Classroom

Science in the Classroom (SitC) is a collection of freely available annotated research papers from the Science family of journals. SitC aims to help educators, undergraduates, and advanced high school students understand the research contained in scientific primary literature by using annotations and providing accompanying teaching materials. Annotations include vocabulary, methods, descriptions of prior research, and explanations of major conclusions. Each paper has an educator's guide outlining connections to science competencies within STEM learning frameworks and standards. Educator guides also provide suggested activities, discussion questions, and resources for further exploration of the subject.

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Sam S Donovan onto HITS 2018 Workshop Resources

Allen Cell Explorer

Using deep learning to illuminate cell structure

The Allen Integrated Cell unites two cutting-edge technologies to visualize and understand the organization of the major organelles and structures that comprise human induced pluripotent stem cells.

​Explore the 3D outputs of these models with our online integrated cell viewer.

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Swirl - for learning R

swirl teaches you R programming and data science interactively, at your own pace, and right in the R console!

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IF-AT: Immediate feedback Assessment Technique

 

Epstein Educational Enterprises has developed a unique multiple-choice learning and assessment system called the Immediate Feedback Assessment Technique, (“IF-AT”). The IF-AT is ideally suited for classroom assessment, textbook and test prep publishers, learning centers, as well as corporate & professional training organizations committed to providing innovative, state-of-the-art learning and teaching tools. 

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Software Carpentry

Since 1998, Software Carpentry has been teaching researchers the computing skills they need to get more done in less time and with less pain. Our volunteer instructors have run hundreds of events for more than 34,000 researchers since 2012. All of our lesson materials are freely reusable under the Creative Commons - Attribution license.

The Software Carpentry Foundation and its sibling project, Data Carpentry, have merged to become The Carpentries, a fiscally sponsored project of Community Initiatives, a 501(c)3 non-profit incorporated in the United States.

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Carlos Christopher Goller onto Data Sources

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