Monthly Archives: April 2019

Scientists who share data publicly receive more citations | Science Codex

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“A new study finds that papers with data shared in public gene expression archives received increased numbers of citations for at least five years. The large size of the study allowed the researchers to exclude confounding factors that have plagued prior studies of the effect and to spot a trend of increasing dataset reuse over time. The findings will be important in persuading scientists that they can benefit directly from publicly sharing their data.

The study, which adds to growing evidence for an open data citation benefit across different scientific fields, is entitled “Data reuse and the open citation advantage”. It was conducted by Dr. Heather Piwowar of Duke University and Dr. Todd Vision of the University of North Carolina at Chapel Hill, and published today in PeerJ, a peer reviewed open access journal in which all articles are freely available to everyone….”

Errors in Time-Series Remote Sensing and an Open Access Application for Detecting and Visualizing Spatial Data Outliers Using Google Earth Engine – IEEE Journals & Magazine

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“Following here is a case of NASA Moderate Resolution Imaging Spectroradiometer (MODIS) time-series vegetation productivity where we observed several substantial inconsistencies among versions of the same product. The anomalies discovered are not isolated to a particular region, persisting across geographies, and occurring at multiple time intervals. In response to these findings, we developed a simple yet effective open access application for detecting and visualizing remote sensing data outliers using the Google Earth Engine platform. …”

Errors in Time-Series Remote Sensing and an Open Access Application for Detecting and Visualizing Spatial Data Outliers Using Google Earth Engine – IEEE Journals & Magazine

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“Following here is a case of NASA Moderate Resolution Imaging Spectroradiometer (MODIS) time-series vegetation productivity where we observed several substantial inconsistencies among versions of the same product. The anomalies discovered are not isolated to a particular region, persisting across geographies, and occurring at multiple time intervals. In response to these findings, we developed a simple yet effective open access application for detecting and visualizing remote sensing data outliers using the Google Earth Engine platform. …”

novel open access web portal for integrating mechanistic and toxicogenomic study results | Toxicological Sciences | Oxford Academic

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Abstract:  Applying toxicogenomics to improving the safety profile of drug candidates and crop protection molecules is most useful when it identifies relevant biological and mechanistic information that highlights risks and informs risk mitigation strategies. Pathway-based approaches, such as GSEA, integrate toxicogenomic data with known biological process and pathways. Network methods help define unknown biological processes and offer data reduction advantages. Integrating the two approaches would improve interpretation of toxicogenomic information. Barriers to the routine application of these methods in genome-wide transcriptomic studies include a need for “hands-on” computer programming experience, the selection of one or more analysis methods (e.g. pathway analysis methods), the sensitivity of results to algorithm parameters, and challenges in linking differential gene expression to variation in safety outcomes. To facilitate adoption and reproducibility of gene expression analysis in safety studies, we have developed Collaborative Toxicogenomics (CTox), an open-access integrated web portal using the Django web framework. The software, developed with the Python programming language, is modular, extensible and implements “best-practice” methods in computational biology. New study results are compared to over 4,000 rodent liver experiments from Drug Matrix and open TG-GATEs. A unique feature of the software is the ability to integrate clinical chemistry and histopathology-derived outcomes with results from gene expression studies, leading to relevant mechanistic conclusions. We describe its application by analyzing the effects of several toxicants on liver gene expression and exemplify application to predicting toxicity study outcomes upon chronic treatment from expression changes in acute-duration studies.

novel open access web portal for integrating mechanistic and toxicogenomic study results | Toxicological Sciences | Oxford Academic

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Abstract:  Applying toxicogenomics to improving the safety profile of drug candidates and crop protection molecules is most useful when it identifies relevant biological and mechanistic information that highlights risks and informs risk mitigation strategies. Pathway-based approaches, such as GSEA, integrate toxicogenomic data with known biological process and pathways. Network methods help define unknown biological processes and offer data reduction advantages. Integrating the two approaches would improve interpretation of toxicogenomic information. Barriers to the routine application of these methods in genome-wide transcriptomic studies include a need for “hands-on” computer programming experience, the selection of one or more analysis methods (e.g. pathway analysis methods), the sensitivity of results to algorithm parameters, and challenges in linking differential gene expression to variation in safety outcomes. To facilitate adoption and reproducibility of gene expression analysis in safety studies, we have developed Collaborative Toxicogenomics (CTox), an open-access integrated web portal using the Django web framework. The software, developed with the Python programming language, is modular, extensible and implements “best-practice” methods in computational biology. New study results are compared to over 4,000 rodent liver experiments from Drug Matrix and open TG-GATEs. A unique feature of the software is the ability to integrate clinical chemistry and histopathology-derived outcomes with results from gene expression studies, leading to relevant mechanistic conclusions. We describe its application by analyzing the effects of several toxicants on liver gene expression and exemplify application to predicting toxicity study outcomes upon chronic treatment from expression changes in acute-duration studies.

Lawyers and law students’ signatures needed for Supreme Court amicus brief in favor of publishing the law / Boing Boing

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“Attentive reader will note that rogue archivist Carl Malamud (previously) published the laws of Georgia — including the paywalled annotations to the state laws — in 2015, prompting the state to sue him and literally call him a terrorist; Malamud countersued in 2015 and won a huge victory in 2018, when the US Court of Appeals for the 11th Circuit ruled that the law could not be copyrighted.

Now, the State of Georgia wants to go to the Supreme Court to argue for its right to charge the people of Georgia to know which laws they are supposed to be following. There’s a lot at stake: Malamud has been threatened by Idaho, Oregon, Mississippi, and the District of Columbia for posting state laws and is being sued by six plaintiffs in DC for posting public safety laws, and has received a dozen more takedowns from Standards Development Organizations whose standards have been incorporated into state law.

Malamud and his counsel (Elizabeth Rader and Tom Goldstein and Eric Citron of Goldstein & Russell),are responding to Georgia’s petition and they are seeking amici: if you are a law student or practicioner they would like you to sign onto this amicus brief prepared by Jeff Pearlman by filling in this form….”

Lawyers and law students’ signatures needed for Supreme Court amicus brief in favor of publishing the law / Boing Boing

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“Attentive reader will note that rogue archivist Carl Malamud (previously) published the laws of Georgia — including the paywalled annotations to the state laws — in 2015, prompting the state to sue him and literally call him a terrorist; Malamud countersued in 2015 and won a huge victory in 2018, when the US Court of Appeals for the 11th Circuit ruled that the law could not be copyrighted.

Now, the State of Georgia wants to go to the Supreme Court to argue for its right to charge the people of Georgia to know which laws they are supposed to be following. There’s a lot at stake: Malamud has been threatened by Idaho, Oregon, Mississippi, and the District of Columbia for posting state laws and is being sued by six plaintiffs in DC for posting public safety laws, and has received a dozen more takedowns from Standards Development Organizations whose standards have been incorporated into state law.

Malamud and his counsel (Elizabeth Rader and Tom Goldstein and Eric Citron of Goldstein & Russell),are responding to Georgia’s petition and they are seeking amici: if you are a law student or practicioner they would like you to sign onto this amicus brief prepared by Jeff Pearlman by filling in this form….”

Revisiting – Navigating the Big Deal: A Guide for Societies – The Scholarly Kitchen

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“In the wake of Plan S, many research society and independent publishers are exploring potential partnerships with larger publishing houses. While Plan S is the catalyst for this activity, it’s part of a longer term trend in the market toward scale as the key advantage leading to success. The benefit for a smaller publisher in such an arrangement is that they gain access to that scale, along with the resources that come with it. The negatives include losing some levels of control over one’s publication program. In particular, as the Big Deal has evolved, it has changed the way these partnerships can work. Because so much effort is currently going into expanding the Big Deal into The Bigger Deal (adding in open access author fees on top of subscription access), I thought it was a good time to revisit Michael Clarke’s post from last year that talked about understanding the current state of the Big Deal and the careful planning one needs to do in order to put together a successful publishing partnership….”

Revisiting – Navigating the Big Deal: A Guide for Societies – The Scholarly Kitchen

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“In the wake of Plan S, many research society and independent publishers are exploring potential partnerships with larger publishing houses. While Plan S is the catalyst for this activity, it’s part of a longer term trend in the market toward scale as the key advantage leading to success. The benefit for a smaller publisher in such an arrangement is that they gain access to that scale, along with the resources that come with it. The negatives include losing some levels of control over one’s publication program. In particular, as the Big Deal has evolved, it has changed the way these partnerships can work. Because so much effort is currently going into expanding the Big Deal into The Bigger Deal (adding in open access author fees on top of subscription access), I thought it was a good time to revisit Michael Clarke’s post from last year that talked about understanding the current state of the Big Deal and the careful planning one needs to do in order to put together a successful publishing partnership….”

All University of California campuses commit to DOAJ – News Service

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“Ten institutions from the University of California – all nine campuses – commit €90,000 to DOAJ, the largest US consortium to support DOAJ via the SCOSS initiative so far.

DOAJ is very pleased for the support received from the University of California towards a sustainable funding model promoted by SCOSS….”

All University of California campuses commit to DOAJ – News Service

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“Ten institutions from the University of California – all nine campuses – commit €90,000 to DOAJ, the largest US consortium to support DOAJ via the SCOSS initiative so far.

DOAJ is very pleased for the support received from the University of California towards a sustainable funding model promoted by SCOSS….”

Linking Open Access Movement to the Indonesian Islamic Higher Education | Atlantis Press

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Abstract:  The Open Access Movement promote disseminate scientific research and data that can be accessed by many parties, both amateur and professional. The research was done to elaborate the relation between the movement and Islamic Higher Education in term of principles and implementation. Through literature study and fieldwork observation, it is found that the spirit of Open Access Movement has already embedded in Islamic Higher Education through volunteerism, openness and selflessness in Indonesian Islamic universities. This movement is also conformable with general Indonesian Islamic education, which has been spread out as the terms: Tuan Guru, Kyai, Buya, Ajengan and other experts Appellation. All have been contributed in spreading knowledge with volunteerism and non-profit. The implementation of Open Access in Islamic Higher Education has been done through Open Journal System and some lecturers in everyday coaching. The openness and free coaching reach the spirit and slogan of Indonesian Ministry of Religion, Ikhlas Beramal (Work with Sincerity).

Linking Open Access Movement to the Indonesian Islamic Higher Education | Atlantis Press

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Abstract:  The Open Access Movement promote disseminate scientific research and data that can be accessed by many parties, both amateur and professional. The research was done to elaborate the relation between the movement and Islamic Higher Education in term of principles and implementation. Through literature study and fieldwork observation, it is found that the spirit of Open Access Movement has already embedded in Islamic Higher Education through volunteerism, openness and selflessness in Indonesian Islamic universities. This movement is also conformable with general Indonesian Islamic education, which has been spread out as the terms: Tuan Guru, Kyai, Buya, Ajengan and other experts Appellation. All have been contributed in spreading knowledge with volunteerism and non-profit. The implementation of Open Access in Islamic Higher Education has been done through Open Journal System and some lecturers in everyday coaching. The openness and free coaching reach the spirit and slogan of Indonesian Ministry of Religion, Ikhlas Beramal (Work with Sincerity).

We invite you to join us in Monemvasia! – Editoria

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“We are ridiculously excited to announce that the next version of Editoria is here! It has everything: 18 community-proposed new features, as well as a complete rebuild of the application against the new PubSweet, upgrade of Wax, enhanced xSweet and extended Paged.js! It’s more functionally elegant, more beautiful, more stable, and faster than its predecessor version….”

We invite you to join us in Monemvasia! – Editoria

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“We are ridiculously excited to announce that the next version of Editoria is here! It has everything: 18 community-proposed new features, as well as a complete rebuild of the application against the new PubSweet, upgrade of Wax, enhanced xSweet and extended Paged.js! It’s more functionally elegant, more beautiful, more stable, and faster than its predecessor version….”