biologist with a computing problem; personal account @__crusoe
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Yaks

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I’d like to teach scientists how to program, but that would be a lot easier to do if we had better software tools to offer them.

I’d like to teach undergraduates how to design better software tools, but that would be a lot easier to do if they knew more about software engineering.

I’d like to teach undergraduates an evidence-based introduction to software engineering, but that would be a lot easier to do if more people knew how to teach well.

I’d like to teach everyone how to teach well, but that would be a lot easier to do if people in power actually valued and rewarded good teaching.

I’d like to teach people who don’t have power where it comes from and how to take it, but—ah. OK, I guess I’ve found the yak I need to shave.

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biocrusoe
103 days ago
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Lansing, MI
luizirber
104 days ago
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Davis, CA
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Revisiting Wonder Woman

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It’s been around a year and a half since I first read The Secret History of Wonder Woman and went on a Wonder Woman reading binge.  Despite reading a decent stack of Wonder Woman comics back then, I never really found a story that resonated with me.  My favorite of …

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biocrusoe
498 days ago
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Lansing, MI
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PSD, The Owner Has Noticed

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In Chinua Achebe's, A Man of the People, the narrator, Odilli,  describes an incident between villagers and a greedy local shopkeeper, Josiah. While disliked by many, the villagers could tolerate his greed as long as the shop remained well-stocked and convenient. But one day Josiah is caught stealing a blind beggar's walking stick. He was planning to use it for a medicine that would "turn [the villagers] into blind buyers of his wares." This act epitomizes Josiah's greed and turns the entire village against him. "Josiah has taken away enough for the owner to notice," a villager says.

"I thought much afterwards about that proverb, about the man taking things away until the owner at last notices. In the mouth of our people there was no greater condemnation. It was not just a simple question of a man's cup being full. A man's cup might be full and none be the wiser. But here the owner knew, and the owner, I discovered, is the will of the whole people." 

If you're wondering why people in Romania are going out to protest, night after night, barely a month into the new government's four year mandate, it's because the owner has finally noticed. 

We all knew about the kick-backs, the graft, the petty bribes. Every city hall and institution in Romania has their share of scandals. This was initially tolerated because, "that's Romania", and, more recently, because Romania's National Anti Corruption Directorate (DNA) are prosecuting more corruption cases than just about anyone else in the world.

The Josiahs in the PSD* think they can use legal loopholes as medicine and immunize themselves against prosecution, while simultaneously blinding the people into acquiescence. 

But, "within one week, Josiah was ruined." Odili tells us.

Let's hope it won't take much longer in Romania.

                                                           See you out there


*PSD is Romania's Social Democratic Party, the heir to Romania's Communist Party, which governed the country during most of its post-communist era. 


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biocrusoe
528 days ago
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Well painted explanation of why Romanians are protesting in historical numbers this week.
Lansing, MI
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European Open Science Cloud (EOSC) Pilot project launched!

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The European Open Science Cloud (EOSC) Pilot project kicked off last 17-18 January in Amsterdam. The EOSCpilot brings together about 50 partners, third-parties and subcontractors to support the development of the European Open Science Cloud (EOSC). It will establish the governance framework for the EOSC and contribute to the development of European open science policy and best practice. Moreover, it will develop a number of working scientific demonstrators that show interoperability and its benefits in a number of scientific domains, by integrating services and infrastructures. Finally, it will engage with a broad range of stakeholders, crossing borders and communities, to build the trust and skills required for adoption of an open approach to scientific research.

The EOSCpilot project aims at addressing some of the key reasons why European research is not yet fully tapping into the potential of data, in particular by reducing the existing geographic, thematic, technological, and governance fragmentation between data infrastructures; by improving interoperability between data infrastructures and demonstrating how data and resources can be shared even when they are large and complex and in varied formats; by providing incentives and other means to enhance openness to data coming from publicly funded research, and; by engaging stakeholders of different scientific communities.

In this way, the EOSC pilot project will improve the ability to reuse data resources and provide an important step towards building a dependable open-data research environment where data from publicly funded research is always open and there are clear incentives and rewards for the sharing of data and resources.

This ambitious project will face challenges related to technology, culture and governance. On the technological side, EOSC will need to provide real interoperability among infrastructures and data, in order to ensure standardisation and services operation. With respect to governance, the EOSCpilot must create an open governance  and policy framework for the EOSC that is inclusive of all stakeholders. However, the most difficult challenge would probably rely in radically changing the culture of researchers and infrastructure managers, engaging them so that to remove obstacles related to the availability of own data and to the use of other’s infrastructures. In this scenario, it would be then vital to collaborate with other relevant initiatives such as OpenAIRE, EUDAT and so on, in order to establish a common ground of infrastructures and interoperability on different levels.

The EOSCpilot will last for 24 months (ending December 2018). The project is organised in 9 work packages, dealing with management and governance, policy drafting, science demonstrators, services, interoperability, skills, engagement and communication, ethics requirements; all of them are strinctly interconnected and will work synergically to build the EOSC ecosystem.

The EOSCpilot will put together some policy expert groups, in order to explore open science drivers and constraints, issues related to data protection and ownerships, ethical driven constraints, and so on, so that to establish the policy framework required for an open and trusted environment. They will also develop a portfolio and roadmap for the EOSC services and define the rules of engagement for service providers.

The pilot will fund and mentor a total of 15 ambitious science demonstrators as proofs-of-concept and prototypes for the ambitious new levels of interoperability the EOSC will bring. 5 have already been selected at project proposal stage, belonging to different research areas from life sciences, energy, climate science, material science and the humanities. Future open calls will bring 10 more demonstrators on board over the course of the next year (watch this space!). Infrastructures wishing to participate to the new expression of interest for science demonstrators should have a strong and defined data analysis activity showing their scientific excellence and societal impact; provide data integration, management, interoperability and analysis that will drive the development of new services within EOSC; be already developed and supported by mature research infrastructures and/or organisations; and last but not least, commit to publish or consuming third party research artifacts.

The EOSCpilot plans to connect with active actors in open data science education, such as schools, universities, pilots and projects dealing with education and training, building training and skills, then, on what already exists. The project will also deliver a series of workshops engaging specific targets of stakeholders, such as researchers, research funders, communities of practice, and to provide training materials useful to improve researchers skills on some hot issues.

Learn more about the project: http://eoscpilot.eu/ (more information coming soon!)

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biocrusoe
535 days ago
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Yeehaw!
Lansing, MI
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Update on signs of fascism in the U.S.

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I took a vacation from updating my signs of fascism spreadsheet and now I’m back with a big picture update. Short version: Trump seems to be failing at one of the most basic requirements of fascism, which is winning popular support and suppressing public dissent.

Trump was sworn in yesterday with the lowest approval ratings of a president-elect since we started measuring approval ratings, and his ratings are still falling. Congressional representatives are still acting like they are worried about getting re-elected, and are changing their votes when their constituents pressure them. The puny attendance and visible lack of enthusiasm at Trump’s inauguration, especially as contrasted with the various protests, is another sign of his failure in this important area. Trump is also failing to recruit artists and pop culture in general, another thing fascist movements are usually at least partly successful in doing.

My conclusion: we’re not currently on the path to total fascism in the U.S. If someone competent takes over the Trump administration (Bannon?), that could change quickly, but as far as I can tell, Trump is fundamentally unwilling to give anyone that level of power. An increase in U.S. fascism is still an imminent danger and something we should be alert for, but I’m feeling more hopeful about the resistance.

The biggest problem with my signs of fascism spreadsheet is that the actions column I created to tell myself what to do – pack, leave, flee, etc. – depends so much on a lot of factors not in the spreadsheet. For me, as a disabled white cis woman living in California who has healthcare through the ACA, things are okay right now, but any changes to the ACA will have a major effect on my safety. For others, many people have left the U.S already; others want to leave and can’t. Trans folks, Black people, Muslims, immigrants both documented and undocumented, disabled folks – we’re all more vulnerable to the upcoming administration. And that’s not reflected in the spreadsheet.

I’ve decided to start tracking four things for myself on a scale of 1 to 10: how much I’m resisting, how much I’m collaborating, what my personal danger is, and how hard emigration is for me personally. My fear is that, like the author of Defying Hitler, I’ll gradually collaborate more and more without realizing it.

The future is still scary and fucked up, and many bad things have happened, are happening, and will continue to happen. I am still working with my immigration lawyer to have options to live and work outside the U.S. I still have a go bag packed. I’m still getting copies of all my identity documents. But I’m also actively involved in resistance movements and I’m seeing the results of our work (including behind-the-scenes changes that I can’t talk about in public). People in the U.S. and around the world are connecting and mobilizing and speaking up.

I’ll close with a quote from Rebecca Solnit:

Many people are still trying to figure out what to do; others are doing it. They give me hope, in some portion of humanity, the portion that will resist Trump and defend our ideals. It will be hard. It will be ugly. Our job will be to be embody and protect all of those things most antithetical to authoritarianism, racism, misogyny, kleptocracy, an atmosphere of lies and indifference to science, fact and truth.

In easy times, we grow slack; this will require us each to find our capacity for heroism. Some will, and my hope lies with them. Or us.


Tagged: fascism, politics



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biocrusoe
539 days ago
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Lansing, MI
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Bookish Apps

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I consider myself a moderate app user.  On my phone, I have some games, social media, health and fitness and entertainment apps.  I use them all occasionally but I don’t consider myself particularly well-versed in any of those app categories.  However, when it comes to bookish apps, I like to …

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biocrusoe
541 days ago
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Lansing, MI
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