Case Studies/A mathematical way to think about biology - Revision history

David Liao: /* Motivations */

2013-03-28T16:02:27Z

Motivations

← Older revision		Revision as of 16:02, 28 March 2013
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	== Motivations ==		== Motivations ==

	Current open access initiatives require journal articles to be accessible free of charge after an embargo period. These mandates achieve "technical" openness. Achieving a more practical openness, however, requires more than uploading a record of ~~text and images~~ to a public repository. The know-how to peruse scientific literature with ease must also be broadly distributed. It is preferable to release ''both'' software ''and'' underlying system libraries under GPL. Speaking loosely along the same lines of sentiment, it is likewise preferable to release, as free cultural works, ''both'' scientific literature ''and'' the instructional materials by virtue of which that literature becomes readable. Releasing the video tutorials under a CC BY-SA license communicates that the mathematical know-how described in these videos is a public good.		Current open access initiatives require journal articles to be accessible free of charge after an embargo period. These mandates achieve "technical" openness. Achieving a more practical openness, however, requires more than uploading a record of research reports to a public repository of overwhelming walls of text and figures. The know-how to peruse scientific literature with ease must also be broadly distributed. It is preferable to release ''both'' software ''and'' underlying system libraries under GPL. Speaking loosely along the same lines of sentiment, it is likewise preferable to release, as free cultural works, ''both'' scientific literature ''and'' the instructional materials by virtue of which that literature becomes readable. Releasing the video tutorials under a CC BY-SA license communicates that the mathematical know-how described in these videos is a public good.

	== Impact of the Creative Commons ==		== Impact of the Creative Commons ==

	One of the videos in the series derives significantly from a research journal article. The author wanted to ask the journal under what licenses he could release the video. A decade ago, this would have required a long email explaining copyleft. Owing to educational outreach by the Creative Commons (and allied efforts by the Free Software Foundation, Wikipedia, and the Public Library of Science), awareness of free culture principles has greatly increased. This made it easy to refer to different licenses according to their abbreviated CC names during discussion with the journal (the journal granted permission to release the video under CC BY-SA).		One of the videos in the series derives significantly from a research journal article. The author wanted to ask the journal under what licenses he could release the video. A decade ago, this would have required a long email explaining copyleft. Owing to educational outreach by the Creative Commons (and allied efforts by the Free Software Foundation, Wikipedia, and the Public Library of Science), awareness of free culture principles has greatly increased. This made it easy to refer to different licenses according to their abbreviated CC names during discussion with the journal (the journal granted permission to release the video under CC BY-SA).

David Liao: /* Overview */

2013-03-28T16:00:44Z

Overview

← Older revision		Revision as of 16:00, 28 March 2013
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	To ensure broadest delivery of this resource, the slides and videos are made available under a CC BY-SA license.		To ensure broadest delivery of this resource, the slides and videos are made available under a CC BY-SA license.

	David Liao is a physicist (PhD, Princeton) in the Physical Sciences-Oncology Network.		The videos are produced by David Liao, a physicist (PhD, Princeton) in the Physical Sciences-Oncology Network.

	== License Usage ==		== License Usage ==

David Liao: /* Overview */

2013-03-28T15:59:29Z

Overview

← Older revision		Revision as of 15:59, 28 March 2013
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	In 2009, the National Cancer Institute began funding the Physical Sciences-Oncology Network to bring physical scientists and biologists together to look at cancer in new ways [http://physics.cancer.gov]. To fully realize the potential benefit of this network, investigators must accomplish more than simply continuing the development of measurement technologies. Moore et al. have commented that previous "contributions [i.e. x-rays, PET, and MRI] leverage the technology development aspect from the physical sciences . . . but not other important aspects like methodology, practices and thought processes. What is different about the NCI’s PS-OC Program is the conviction that unique physical sciences and engineering approaches and principles can be integrated . . . in cancer research to yield a more fundamental understanding of the disease" [http://iopscience.iop.org/1478-3975/8/1/010302].		In 2009, the National Cancer Institute began funding the Physical Sciences-Oncology Network to bring physical scientists and biologists together to look at cancer in new ways [http://physics.cancer.gov]. To fully realize the potential benefit of this network, investigators must accomplish more than simply continuing the development of measurement technologies. Moore et al. have commented that previous "contributions [i.e. x-rays, PET, and MRI] leverage the technology development aspect from the physical sciences . . . but not other important aspects like methodology, practices and thought processes. What is different about the NCI’s PS-OC Program is the conviction that unique physical sciences and engineering approaches and principles can be integrated . . . in cancer research to yield a more fundamental understanding of the disease" [http://iopscience.iop.org/1478-3975/8/1/010302].

	One of these physical sciences "thought processes" is quantitative reasoning. Resources for developing this skill currently include introductory courses in quantitative biology. For example, Los Alamos National Laboratories hosts the invaluable q-Bio summer school [http://q-bio.org]. However, mathematical prerequisites for these courses remain a ~~challenge~~ for investigators trained in many life sciences fields.		One of these physical sciences "thought processes" is quantitative reasoning. Resources for developing this skill currently include introductory courses in quantitative biology. For example, Los Alamos National Laboratories hosts the invaluable q-Bio summer school [http://q-bio.org]. However, mathematical prerequisites for these courses remain a difficulty for investigators trained in many life sciences fields.

	''A mathematical way to think about biology'' was developed to help address this challenge. The website is a collection of video tutorials to help biologists, clinicians, and patient advocates prepare for courses in quantitative biology [http://qbio.lookatphysics.com]. The purpose of these videos is to provide familiarity with introductory topics often presented in quantitative biology courses and confidence to actively learn the more sophisticated concepts that are developed from these foundations.		''A mathematical way to think about biology'' was developed to help address this challenge. The website is a collection of video tutorials to help biologists, clinicians, and patient advocates prepare for courses in quantitative biology [http://qbio.lookatphysics.com]. The purpose of these videos is to provide familiarity with introductory topics often presented in quantitative biology courses and confidence to actively learn the more sophisticated concepts that are developed from these foundations.

David Liao: /* Motivations */

2013-03-28T15:57:06Z

Motivations

← Older revision		Revision as of 15:57, 28 March 2013
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	== Motivations ==		== Motivations ==

	Current open access initiatives require journal articles to be accessible free of charge after an embargo period. These mandates achieve "technical" openness. Achieving a more practical openness, however, requires more than uploading a record of text and images to a public repository. The know-how to peruse scientific literature with ease must also be broadly distributed. It is preferable to release ''both'' software ''and'' underlying system libraries under GPL. Speaking loosely along the same lines of sentiment, it is likewise preferable to release ''both'' scientific literature ~~and datasets~~ ''and'' the instructional materials ~~that make~~ that literature readable ~~as free cultural works~~. Releasing the video tutorials under a CC BY-SA license communicates that the mathematical know-how described in these videos is a public good.		Current open access initiatives require journal articles to be accessible free of charge after an embargo period. These mandates achieve "technical" openness. Achieving a more practical openness, however, requires more than uploading a record of text and images to a public repository. The know-how to peruse scientific literature with ease must also be broadly distributed. It is preferable to release ''both'' software ''and'' underlying system libraries under GPL. Speaking loosely along the same lines of sentiment, it is likewise preferable to release, as free cultural works, ''both'' scientific literature ''and'' the instructional materials by virtue of which that literature becomes readable. Releasing the video tutorials under a CC BY-SA license communicates that the mathematical know-how described in these videos is a public good.

	== Impact of the Creative Commons ==		== Impact of the Creative Commons ==

	One of the videos in the series derives significantly from a research journal article. The author wanted to ask the journal under what licenses he could release the video. A decade ago, this would have required a long email explaining copyleft. Owing to educational outreach by the Creative Commons (and allied efforts by the Free Software Foundation, Wikipedia, and the Public Library of Science), awareness of free culture principles has greatly increased. This made it easy to refer to different licenses according to their abbreviated CC names during discussion with the journal (the journal granted permission to release the video under CC BY-SA).		One of the videos in the series derives significantly from a research journal article. The author wanted to ask the journal under what licenses he could release the video. A decade ago, this would have required a long email explaining copyleft. Owing to educational outreach by the Creative Commons (and allied efforts by the Free Software Foundation, Wikipedia, and the Public Library of Science), awareness of free culture principles has greatly increased. This made it easy to refer to different licenses according to their abbreviated CC names during discussion with the journal (the journal granted permission to release the video under CC BY-SA).

David Liao: /* Motivations */

2013-03-28T15:55:21Z

Motivations

← Older revision		Revision as of 15:55, 28 March 2013
Line 33:		Line 33:
	== Motivations ==		== Motivations ==

	Current open access initiatives require journal articles to be accessible free of charge after an embargo period. These mandates achieve "technical" openness. Achieving a more practical openness, however, requires more than uploading a record of text and images to a public repository. The know-how to peruse scientific literature with ease must also be broadly distributed. Releasing the video tutorials under a CC BY-SA license communicates that ~~this~~ mathematical know-how is a public good.		Current open access initiatives require journal articles to be accessible free of charge after an embargo period. These mandates achieve "technical" openness. Achieving a more practical openness, however, requires more than uploading a record of text and images to a public repository. The know-how to peruse scientific literature with ease must also be broadly distributed. It is preferable to release ''both'' software ''and'' underlying system libraries under GPL. Speaking loosely along the same lines of sentiment, it is likewise preferable to release ''both'' scientific literature and datasets ''and'' the instructional materials that make that literature readable as free cultural works. Releasing the video tutorials under a CC BY-SA license communicates that the mathematical know-how described in these videos is a public good.

	== Impact of the Creative Commons ==		== Impact of the Creative Commons ==

	One of the videos in the series derives significantly from a research journal article. The author wanted to ask the journal under what licenses he could release the video. A decade ago, this would have required a long email explaining copyleft. Owing to educational outreach by the Creative Commons (and allied efforts by the Free Software Foundation, Wikipedia, and the Public Library of Science), awareness of free culture principles has greatly increased. This made it easy to refer to different licenses according to their abbreviated CC names during discussion with the journal (the journal granted permission to release the video under CC BY-SA).		One of the videos in the series derives significantly from a research journal article. The author wanted to ask the journal under what licenses he could release the video. A decade ago, this would have required a long email explaining copyleft. Owing to educational outreach by the Creative Commons (and allied efforts by the Free Software Foundation, Wikipedia, and the Public Library of Science), awareness of free culture principles has greatly increased. This made it easy to refer to different licenses according to their abbreviated CC names during discussion with the journal (the journal granted permission to release the video under CC BY-SA).

David Liao at 15:47, 28 March 2013

2013-03-28T15:47:28Z

← Older revision		Revision as of 15:47, 28 March 2013
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	{{Case Study		{{Case Study
	\|Description=Video ~~tutorial series~~ to help researchers, clinicians, patient advocates~~, and the public~~ learn about mathematical thinking at the interface of the physical sciences and biology, released under a Creative Commons Attribution-Share Alike license.		\|Description=Video tutorials to help researchers, clinicians, and patient advocates learn about mathematical thinking at the interface between the physical sciences and biology, released under a Creative Commons Attribution-Share Alike license.
	\|Mainurl=http://qbio.lookatphysics.com		\|Mainurl=http://qbio.lookatphysics.com
	\|Author=David Liao		\|Author=David Liao
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	\|Country=global		\|Country=global
	\|Quote=Excellent site for both basic and advanced lessons on applying mathematics to biology		\|Quote=Excellent site for both basic and advanced lessons on applying mathematics to biology
	\|Quote_Attribution=Tweeted by the National Cancer Institute Office of Physical Sciences-Oncology ~~(2013 Feb 20)~~		\|Quote_Attribution=Tweeted by the National Cancer Institute Office of Physical Sciences-Oncology [https://twitter.com/NCIPhySci/status/304250851193655296]
	\|Image_Header=http://wiki.creativecommons.org/images/4/45/LookatphysicsHeader.png		\|Image_Header=http://wiki.creativecommons.org/images/4/45/LookatphysicsHeader.png
	\|Image_attribution=David Liao		\|Image_attribution=Screenshot of lookatphysics.com (David Liao)
	\|Image_license=http://creativecommons.org/licenses/by-sa/3.0/		\|Image_license=http://creativecommons.org/licenses/by-sa/3.0/
	}}		}}
Line 25:		Line 25:
	To ensure broadest delivery of this resource, the slides and videos are made available under a CC BY-SA license.		To ensure broadest delivery of this resource, the slides and videos are made available under a CC BY-SA license.

	David Liao is a physicist ~~by training~~ (PhD, Princeton) in the Physical Sciences-Oncology Network.		David Liao is a physicist (PhD, Princeton) in the Physical Sciences-Oncology Network.

	== License Usage ==		== License Usage ==
Line 33:		Line 33:
	== Motivations ==		== Motivations ==

	Current open access initiatives ~~in research~~ achieve "technical" openness. ~~Journal articles are available for viewing without charge. To achieve actual~~ openness, however, ~~knowledge cannot merely be uploaded as~~ a ~~mass~~ of text and images to a public repository. The know-how to peruse it with ease must also be broadly distributed. Releasing the video tutorials ~~series~~ under CC BY-SA ~~is my way of communicating~~ that this ~~knowledge belongs to everyone~~.		Current open access initiatives require journal articles to be accessible free of charge after an embargo period. These mandates achieve "technical" openness. Achieving a more practical openness, however, requires more than uploading a record of text and images to a public repository. The know-how to peruse scientific literature with ease must also be broadly distributed. Releasing the video tutorials under a CC BY-SA license communicates that this mathematical know-how is a public good.

	== Impact of the Creative Commons ==		== Impact of the Creative Commons ==

	One of the videos ~~is derived~~ significantly from a research journal article. I wanted to ask ~~them~~ under what licenses I could release the video. A decade ago, this would have required a long email explaining copyleft. Owing to educational outreach by the Creative Commons (and allied efforts by the Free Software Foundation, Wikipedia, and the Public Library of Science), awareness of free culture principles has greatly increased. This made it easy ~~for the journal and me~~ to refer to different licenses according to their abbreviated CC names (~~they~~ granted permission to release the video under CC BY-SA).		One of the videos in the series derives significantly from a research journal article. The author wanted to ask the journal under what licenses he could release the video. A decade ago, this would have required a long email explaining copyleft. Owing to educational outreach by the Creative Commons (and allied efforts by the Free Software Foundation, Wikipedia, and the Public Library of Science), awareness of free culture principles has greatly increased. This made it easy to refer to different licenses according to their abbreviated CC names during discussion with the journal (the journal granted permission to release the video under CC BY-SA).

David Liao: /* Impact of the Creative Commons */

2013-03-27T20:21:57Z

Impact of the Creative Commons

← Older revision		Revision as of 20:21, 27 March 2013
Line 37:		Line 37:
	== Impact of the Creative Commons ==		== Impact of the Creative Commons ==

	One of the videos is derived significantly from a research journal article. I wanted to ask them under what licenses I could release the video. A decade ago, this would have required a long email explaining copyleft. Owing to educational outreach by the Creative Commons (and allied efforts by the Free Software Foundation, Wikipedia, and the Public Library of Science), awareness of ~~copyleft~~ principles has greatly increased. This made it easy for the journal and me to refer to different licenses according to their abbreviated CC names (they granted permission to release the video under CC BY-SA).		One of the videos is derived significantly from a research journal article. I wanted to ask them under what licenses I could release the video. A decade ago, this would have required a long email explaining copyleft. Owing to educational outreach by the Creative Commons (and allied efforts by the Free Software Foundation, Wikipedia, and the Public Library of Science), awareness of free culture principles has greatly increased. This made it easy for the journal and me to refer to different licenses according to their abbreviated CC names (they granted permission to release the video under CC BY-SA).

David Liao: /* Overview */

2013-03-27T20:05:50Z

Overview

← Older revision		Revision as of 20:05, 27 March 2013
Line 21:		Line 21:
	One of these physical sciences "thought processes" is quantitative reasoning. Resources for developing this skill currently include introductory courses in quantitative biology. For example, Los Alamos National Laboratories hosts the invaluable q-Bio summer school [http://q-bio.org]. However, mathematical prerequisites for these courses remain a challenge for investigators trained in many life sciences fields.		One of these physical sciences "thought processes" is quantitative reasoning. Resources for developing this skill currently include introductory courses in quantitative biology. For example, Los Alamos National Laboratories hosts the invaluable q-Bio summer school [http://q-bio.org]. However, mathematical prerequisites for these courses remain a challenge for investigators trained in many life sciences fields.

	''A mathematical way to think about biology'' was developed to help address this challenge. The website~~, [http://qbio.lookatphysics.com],~~ is a collection of video tutorials to help biologists, clinicians, and patient advocates prepare for courses in quantitative biology. The purpose of these videos is to provide familiarity with introductory topics often presented in quantitative biology courses and confidence to actively learn the more sophisticated concepts that are developed from these foundations.		''A mathematical way to think about biology'' was developed to help address this challenge. The website is a collection of video tutorials to help biologists, clinicians, and patient advocates prepare for courses in quantitative biology [http://qbio.lookatphysics.com]. The purpose of these videos is to provide familiarity with introductory topics often presented in quantitative biology courses and confidence to actively learn the more sophisticated concepts that are developed from these foundations.

	To ensure broadest delivery of this resource, the slides and videos are made available under a CC BY-SA license.		To ensure broadest delivery of this resource, the slides and videos are made available under a CC BY-SA license.

David Liao: /* Overview */

2013-03-27T20:05:15Z

Overview

← Older revision		Revision as of 20:05, 27 March 2013
Line 21:		Line 21:
	One of these physical sciences "thought processes" is quantitative reasoning. Resources for developing this skill currently include introductory courses in quantitative biology. For example, Los Alamos National Laboratories hosts the invaluable q-Bio summer school [http://q-bio.org]. However, mathematical prerequisites for these courses remain a challenge for investigators trained in many life sciences fields.		One of these physical sciences "thought processes" is quantitative reasoning. Resources for developing this skill currently include introductory courses in quantitative biology. For example, Los Alamos National Laboratories hosts the invaluable q-Bio summer school [http://q-bio.org]. However, mathematical prerequisites for these courses remain a challenge for investigators trained in many life sciences fields.

	''A mathematical way to think about biology'' was developed to help address this challenge. ~~This~~ website is a collection of video tutorials to help biologists, clinicians, and patient advocates prepare for courses in quantitative biology. The purpose of these videos is to provide familiarity with introductory topics often presented in quantitative biology courses and confidence to actively learn the more sophisticated concepts that are developed from these foundations.		''A mathematical way to think about biology'' was developed to help address this challenge. The website, [http://qbio.lookatphysics.com], is a collection of video tutorials to help biologists, clinicians, and patient advocates prepare for courses in quantitative biology. The purpose of these videos is to provide familiarity with introductory topics often presented in quantitative biology courses and confidence to actively learn the more sophisticated concepts that are developed from these foundations.

	To ensure broadest delivery of this resource, the slides and videos are made available under a CC BY-SA license.		To ensure broadest delivery of this resource, the slides and videos are made available under a CC BY-SA license.

David Liao: /* Overview */

2013-03-27T19:59:03Z

Overview

← Older revision		Revision as of 19:59, 27 March 2013
Line 17:		Line 17:
	== Overview ==		== Overview ==

	In 2009, the National Cancer Institute began funding the Physical Sciences-Oncology Network to bring physical scientists together ~~with biologists~~ to look at cancer in new ways [http://physics.cancer.gov]. To fully realize the potential benefit of this network, investigators must accomplish more than simply continuing the development of measurement technologies. Moore et al. have commented that previous "contributions [i.e. x-rays, PET, and MRI] leverage the technology development aspect from the physical sciences . . . but not other important aspects like methodology, practices and thought processes. What is different about the NCI’s PS-OC Program is the conviction that unique physical sciences and engineering approaches and principles can be integrated . . . in cancer research to yield a more fundamental understanding of the disease." [http://iopscience.iop.org/1478-3975/8/1/010302]		In 2009, the National Cancer Institute began funding the Physical Sciences-Oncology Network to bring physical scientists and biologists together to look at cancer in new ways [http://physics.cancer.gov]. To fully realize the potential benefit of this network, investigators must accomplish more than simply continuing the development of measurement technologies. Moore et al. have commented that previous "contributions [i.e. x-rays, PET, and MRI] leverage the technology development aspect from the physical sciences . . . but not other important aspects like methodology, practices and thought processes. What is different about the NCI’s PS-OC Program is the conviction that unique physical sciences and engineering approaches and principles can be integrated . . . in cancer research to yield a more fundamental understanding of the disease" [http://iopscience.iop.org/1478-3975/8/1/010302].

	One of these physical sciences "thought processes" is quantitative reasoning. Resources for developing this skill currently include introductory courses in quantitative biology. For example, Los Alamos National Laboratories hosts the invaluable q-Bio summer school [http://q-bio.org]. However, mathematical prerequisites for these courses remain a challenge for investigators trained in many life sciences fields.		One of these physical sciences "thought processes" is quantitative reasoning. Resources for developing this skill currently include introductory courses in quantitative biology. For example, Los Alamos National Laboratories hosts the invaluable q-Bio summer school [http://q-bio.org]. However, mathematical prerequisites for these courses remain a challenge for investigators trained in many life sciences fields.