The Human Protein Atlas

“The Human Protein Atlas is a Swedish-based program initiated in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome….The Human Protein Atlas program has already contributed to several thousands of publications in the field of human biology and disease and it is selected by the organization ELIXIR (www.elixir-europe.org) as a European core resource due to its fundamental importance for a wider life science community. The Human Protein Atlas consortium is funded by the Knut and Alice Wallenberg Foundation….”

The Human Protein Atlas

“The Human Protein Atlas is a Swedish-based program initiated in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome….The Human Protein Atlas program has already contributed to several thousands of publications in the field of human biology and disease and it is selected by the organization ELIXIR (www.elixir-europe.org) as a European core resource due to its fundamental importance for a wider life science community. The Human Protein Atlas consortium is funded by the Knut and Alice Wallenberg Foundation….”

PCI Evol Biol

“Peer Community in Evolutionary Biology (PCI Evol Biol) has been launched in January 2017. It is a community of 339 recommenders playing the role of editors who recommend unpublished preprints based on peer-reviews to make them complete, reliable and citable articles, without the need for publication in ‘traditional’ journals. Evaluation and recommendation by PCI Evol Biol are free of charge. When a recommender decides to recommend a preprint, he/she writes a recommendation text that is published along with all the editorial correspondence (reviews, recommender’s decisions, authors’ replies) by PCI Evol Biol. The preprint itself is not published by PCI Evol Biol; it remains in the preprint server where it has been posted by the authors. PCI Evol Biol recommenders can also recommend, but to a lesser extent, postprints….”

FAIRDOM

“Do you want to get the most impact from your research?   Are you tired of searching through old computer files to find the methods and data that link together?   Do you want to showcase your research from your best publications?  

FAIRDOM helps you to be in control of collecting, managing, storing, and publishing your data, models, and operating procedures. 

Join the hundreds of researchers who have improved research management practices in their lab, and for themselves using our software and expertise. …”

Addgene Depositors Get More Citations

“Professor Feng Zhang’s original 2013 gene editing paper on CRISPR/Cas amassed nearly 2,400 citations in its first four years (1). In addition to publishing in Science, Professor Zhang deposited the associated plasmids with Addgene. Since then, Addgene has filled over 6,500 requests for these plasmids. While clearly an outlier, this story had us wondering: is there a larger trend here? Do papers associated with Addgene deposits accumulate more citations than those without Addgene deposits? Even more interestingly, could we tell if depositing a plasmid with Addgene causes a paper to get cited more? …So what do we find [from Web of Science]? Lots more citations for the papers with plasmids deposited at Addgene – typically about four times as many as papers without plasmids deposited with Addgene….”

Swiss-born rebranded Alpine Entomology journal joins Pensoft’s open access portfolio | EurekAlert! Science News

“Launched about a century and a half ago, the Swiss Entomological Society’s official journal Die Mitteilungen der Schweizerischen Entomologischen Gesellschaft (Journal of the Swiss Entomological Society) is the latest historical scientific journal to join the lines of Pensoft’s portfolio. As a result of an unanimous vote at the Swiss Entomological Society’s general assembly in March, the journal is now rebranded as Alpine Entomology to reflect the shift in its scope and focus. Furthermore, the renowned journal is also changing its format, submission and review process, “in accordance with the standards of modern scientific publishing”, as explained in the inaugural Editorial.”

Chance discovery of forgotten 1960s ‘preprint’ experiment

“For years, scientists have complained that it can take months or even years for a scientific discovery to be published, because of the slowness of peer review. To cut through this problem, researchers in physics and mathematics have long used “preprints” – preliminary versions of their scientific findings published on internet servers for anyone to read. In 2013, similar services were launched for biology, and many scientists now use them. This is traditionally viewed as an example of biology finally catching up with physics, but following a chance discovery in the archives of Cold Spring Harbor Laboratory, Matthew Cobb, a scientist and historian at the University of Manchester, has unearthed a long-forgotten experiment in biology preprints that took place in the 1960s, and has written about them in a study publishing 16 November in the open access journal PLOS Biology.”

The original preprint system was scientists sharing photocopies

“The movement to make biology papers freely available before they have been peer-reviewed, let alone published in a reputable journal, finally succeeded in 2013, when bioRxiv (pronounced bio-archive) was launched by Cold Spring Harbor Laboratory. But 50 years before, the National Institutes of Health tried something similar: distributing unpublished scientific papers, or preprints, to a handpicked group of leading researchers.”

“Patent-Based Open Science” by Lee Petherbridge

Abstract:  The contemporary approach to innovation in the life sciences relies on a patent-based proprietary model. Limitations on patent rights and business concerns often focus innovation to markets where the near-term monetary rewards are highest. This is “efficient” under an austere understanding of the term, but the proprietary model can be problematic from a practical perspective because it may not focus innovation to certain deserving markets. This Article contends that the property rights conferred by patent law may still serve as a positive base for innovation directed to underserved markets. The comparatively strong rights conferred by patent law provide upstream or pioneering innovators the power to establish some of the environmental conditions in which subsequent innovation takes place. This includes a power to create an environment of relatively open access to rights, which in appropriate cases may foster efficiency gains, reduce innovation suppressive costs, and achieve production for ultimate consumers at closer to marginal cost. In several parts, this paper discusses the topography of law and innovation in the life sciences, the characteristics of innovation in the life sciences that may support the use of patents to impose an “open science” framework, a legal means of imposing such a framework using servitudes, and some of the legal and economic implications of using patents in this manner. This Article concludes that there are reasons why universities and research-oriented medical schools should sometimes favor this approach and that limited testing should be performed to determine the efficacy of the approach.

Addgene: Homepage

“Addgene is a global, nonprofit repository that was created to help scientists share plasmids. Plasmids are DNA-based research reagents commonly used in the life sciences. When scientists publish research papers, they deposit their associated plasmids at Addgene. Then, when other scientists read the publication, they have easy access to the plasmids needed to conduct future experiments. Before Addgene, scientists were tasked with repeatedly shipping plasmids to each new requesting scientist. Now, scientists ship their plasmids to Addgene once, and we take care of the quality control, MTA compliance, shipping, and record-keeping.

For scientists looking to use plasmids, Addgene provides a searchable database of high-quality plasmids, pooled libraries, and plasmid kits, available at affordable prices. All plasmids in Addgene’s repository are sequenced for quality control purposes and tracked with barcodes from the time they arrive at our facility until they are packed for shipment. Scientists can request plasmids through Addgene’s online ordering system. As of 2016, Addgene also provides ready-to-use AAV and lentivirus preparations of commonly requested plasmids as a service to scientists….”