reviews (4 out of 4)

Review of "Utilising Semantic Web Ontologies to publish Experimental Workflows"

In reply to: https://openscience.adaptcentre.ie/publications/2017/eswc/

I can see how the ultimate goal described by the article - to publish semantic representations of experimental workflows - contributes towards the vision of decentralised scholarly communication. Unfortunately I'm missing how the work described in the article contributes towards this ultimate goal. The abstract says you want to see how semantic workflow creation can "be combined with traditional forms of documentation and publication" but I don't see a result pertaining to this.

To begin with, the purpose of the tool is quite narrow. How do you know for sure that "advancing knowledge about the use of vocabularies in facilitating sharing and repeatability of experiments and replication of results" ultimately contributes towards reproducability of results, which is the high level goal of this work? How does knowledge of OPMW tie in with the authoring or experimentation process, for example? Are researchers expected to document their workflows as they go along, or retrospectively after the fact (I imagine this depends on the task at hand). For which stage is your tool intended? Or is it simply a teaching tool rather than designed for actually documenting workflows? This isn't clear.

I thought I might understand better by running the tool, but it seems to be broken.

I'm skeptical about the open world assumption and the "nature of Linked Data" being used as a reason to not provide any instruction for using the tool... I would have thought that whether instruction is needed is a UI concern.

There is no results or analysis section, and the tense makes it sound like the described experiment hasn't actually been carried out. Are you asking for feedback about the design of the experiment? If so, you should state this clearly in the introduction and abstract. if not then I'd like to read this again when your findings are ready.

The background work sections appear to be fairly comprehensive, but this is not my area of expertise, so if there is related work or other background information missing I am unable to point it out. It's not entirely clear how all of the related work describe relates to the problem at hand though so I'd like to see this be made explicit.

The discussion about nuances of licensing is interesting, for example licensing different parts of a workflow separately, and conveying this to people who want to replicate experiments and use the data produced. I think maybe the licensing topic deserves an article and experiment all of its own. Colour coding or different levels of alerts for different licensing to help people understand is an interesting UI challenge. I think ongoing work on Data Terms of Use might be interesting to you (this is about personal data rather than experimental data).

In summary, the stated goals make this worth further discussion, but it's not clear how the work you've done so far meets these goals. I'd like to know what are your next steps forward for this work, and technically how this could integrate with other projects related to exposing more semantically enriched academic research to the world.

🏷 academic publishing edsc2017 linked research reviews semantic web

Sat 27th of May 2017 at 6:35pm (+02:00)

Review of "Decentralized creation of academic documents using a Network Attached Storage (NAS) server"

In reply to: https://www.fiduswriter.org/2017/05/24/decentralized-creation-of-academic-documents-using-a-network-attached-storage-nas-server/

This article addresses quite a specific problem: collaborative document editing without third-party servers. The reasons for not wanting to rely on Web servers, even if they're under the control of the document author, is fairly well explained and motivated.

Addressing authoring solutions to MS Word users is diving in the deep end, but a worthy goal as this reaches a lot of researchers. However, I question that the idea of installing software is too complicated for most people.. do you not think it's possible to get the installation process for FW to be as simple as for MSWord?

I realise that this article is not about FidusWriter, but rather collaborative document editing via a NAS, but it would be helpful to explain more about what FidusWriter does and how it is normally run, ie. not on a NAS, and some comparison.

The authors seem to feel strongly about data ownership, mentioning privacy potentially being violated by corporations and governments. It's not clear however that FidusWriter provides a publishing solution, only an authoring solution. That is, once an article is finished it seems that a PDF is exported and turned over to third parties anyway? Relatedly, I would love to know more about how the authors envision this fitting in with the rest of the scholarly communication process, as mentioned in the abstract, particularly peer-review. Could a similar setup be purposed to permit reviewers to control their review contents as well? I assume FidusWriter takes care of access control, citations, formulas and figures, though the article does not state that.

The article mentions that there are other web services for academic authoring, but doesn't name any. I'd be interested to know which ones the authors analysed. Is it only the ones in the footnote? In which case only Authorea and Overleaf are problematic in the ways mentioned for running on third-party servers. I don't really see evidence that the authors have performed a comprehensive search for alternatives in this space. There are certainly clientside document authoring applications which run on personal data stores, such as Laverna which can talk to RemoteStorage servers, and dokieli (which I'm pretty sure the authors have heard of) which can talk to LDP servers, not to mention 'decentralised Google Docs' type things like NextCloud and CosyCloud. It would be worth finding out how easily any of these could be extended to add collaborative editing if they don't have it already, since they have the decentralisation part covered.

Thus, perhaps it's worth comparing running FidusWriter on a NAS to running various generic personal datastores. It seems to me that FidusWriter rather ties the editing application with the storage, which prevents the user from easily switching applications. It's not clear if FW follows a standard protocol for data exchange with the server either. These aren't really the problems of the authors in this context, but it is a downside of a non-standard system even if it's open source and installed on the user's machine. Useful future work might be taking the idea of a NAS forward with other storage/server and client/application options.

That said, I would love to see a docker image prepared to easily set up FidusWriter on any server, if that doesn't already exist!

Limitations are appropriately mentioned as cost and power of NAS devices, though no specifics are given.

Finally, the authors assume a status-quo vision of academic authoring (eg. the "need" for blind peer review) and proceed from there with a decentralisation angle. More interesting would be a paragraph or two about how an approach like this is setting the stage for future advancement in the space. I like the idea of meeting in the middle; addressing immediate problems authors have with their current tooling, whilst laying some foundations for progressing in the direction opened up to us by Web technologies.

Minor comment: what is meant by "Linux boxes" (in quotes)? Are you getting at things like Raspberry Pis?

And I can't help but ask: did you collaboratively author this article using FidusWriter on a NAS? Some screenshots of doing so would add a whole new layer of credibility to your analysis :)

🏷 academic publishing authoring decentralisation fidus writer linked research reviews https://linkedresearch.org/

Sat 27th of May 2017 at 5:05pm (+02:00)

A response to "Scholarly Social Machines"

In reply to: http://www.oerc.ox.ac.uk/sites/default/files/users/user384/scholarly-social-machines.html

This article looks at the scholarly communication ecosystem through the lens of social machines; something I have thought about a lot but only partially articulated through my contributions to Linked Research. In particular, the hypothesis that we are struggling to improve the state of scholarly communication despite advancements in technology because we are trapped in a machine we have ceased to see is interesting. I've had many conversations with people over the last couple of years who balk at any suggestion of a radical upheaval of scholarly communication, hiding behind notions of futility of incentivising researchers to do anything other than pubish or persih, the immovability of the for-profit publishing industry. They complain about the state of things, yet are transfixed by the status quo. I think that framing this problem as a 'trap' will perhaps nudge folks into looking for a way out, and social machines is a useful concept to work with, something very demonstrably real in other domains, and this might help with finding a perspective on scholarly communication.

The article mentions the 'ecosystem' and lists some of the stages. I think it's worth noting that in Linked Research: An Approach for Scholarly Communication we characterised the different stages, roles and actors in scholarly communication in detail (there's even a diagram!). It's important because this is a hard problem, too big a space, to talk about all at once, and breaking it down into smaller chunks that nonetheless interlink (and the interlinking is critical) can help.

Dave writes that we see the same articles about how to improve being published over and over again, and this is true. I assembled a collection of some of them here. People lament that it's too hard to change, and us Linked Research-y types release software and publish our work in a Webby decentralised way (just like Dave has done, for the version of his article that I'm reading) and shove it under peoples' noses and cry that here is the proof that it's not too hard, and if only a few more people would bother we could iron out the wrinkles and make it easier and easier for everyone to participate. It's catching on, but agonisingly slowly. Most people still smile sadly, with a look of concern about the non-future of our academic careers. Dave writes of the "Catch-22" of using traditional publishing to try to solve some of the problems; and it's true. Even csarven is pushing 'papers' to academic conferences about Linked Research and related tooling in the hopes that academics will pay attention (and so he can get his PhD within this broken system). We console ourselves that at least the PDFs were generated from HTML and CSS, and a link to an open access Web version remains in the abstract even from behind Springer's paywall. Yet somehow the dual effort of publishing 'properly' and demonstrating alternatives is still not ticking the right boxes! What's up with that? So we need a new tactic, and the questions raised in this article are pragmatic and challenging, and a step in the right direction.

Question 8 is important because I often find that when we provocatively push "extreme decentralisation" via Linked Research, people push back against that as too difficult, too flakey, underdeveloped. We're arguing from this end of the spectrum because we're fighting against the very other end right now. But it is a spectrum, and better - more robust, more powerful - would be something in between. One example: the response that an individual can't possibly be counted on to keep their research online for eternity ignores the roles libraries and institutions (and indeed traditional publishers) can play in archiving and indexing work over time.

Another note to reinforce the importance of stepping outside to look in at scholarly communication: people, mostly software engineers, with whom I work on decentralised Social Web technologies look on at academia with confoundment. People claiming to be Web Scientists are putting PDFs behind paywalls? Life-saving medical research is accessible to what percentage of human beings? It seems obvious to the outside that we're really screwing things up here. Dave implies that we need to push people towards revolution over evolution, but we need to open a few more eyes before this can happen.

So how do we get people to step outside and look back in? This article doesn't address this. Arguably the people who will show up to Dave's presentation of this are already eyes-open, so perhaps together we can scheme to break the spell that the status quo holds over others.

Framing this (improving the scholarly comms ecosystem) as an interdisciplinary research problem could be emphasised more. Certainly we could solve all of the technical problems, but the social and political ones remain. I hope that we can take some inspiration from SOCIAM in tackling this in the years to come.

🏷 academic publishing edsc2017 linked research reviews social machines https://linkedresearch.org/

Sat 27th of May 2017 at 3:47pm (+02:00)

Reviews make the world go round

Food in Kobe

Modernark

All vegetarian, mostly vegan, but many non-vegan desserts and drinks. Well labelled on the menu.

I went here twice, once with a fairly big group of carnivores who were reasonably impressed or at least polite about it. It's open late which is a plus, has a nice atmosphere, and free wifi (you have to ask for the password, when I was there it was 88888888). They also sell some organic groceries, vegan cookies, etc.

Food was delicious and portion sizes were reasonable. I tried the vegetarian plate (a selection of things), teriyaka wrap (contains wheat gluten and salad), and a curry and rice bowl. All dishes come with salads and soups. I also had a vegan lassi which was an unusual (but delicious) raspberry flavour, and coconut 'tiramisu' cake, which wasn't really like tiramisu, but was delicious anyway.

Pricey in general, but average for the area.

Natural House Food Court

Tried to go here twice. The first time, though HappyCow says it's open until 2000, they told me they close at 1600. The grocery store part is open later, just not the restaurant. The second time I got there at about 1430 and they told me they'd sold out of curry. Oh well. Picked up some snacks from the store instead, which is extensive and healthy organic produce, though not cheap.

Pink Weed

All vegan, and proud.

Loved this place, but maybe by this point the lack of options in Kobe was wearing on me. It's frustrating that it's only open for lunchtime. There's no wifi, but comfy seating and graphic novels and books to read. I went twice anyway and got a different lunch set each time. The curry was excellent, and more filling than it looked. The sandwich was interesting, I'm not sure what was in it, but it did the job. Accompanying salads and soups were great. I tried cheesecake and poundcake, and chai and iced black tea. Again, pricey in general but normal for this kind of place.

It's also about a 15 minute walk from Sannomiya station, which is handy. Follow the trainline west (mountains on your right) until you reach the next station, then it's off a side road.

Vegan dessert stall

Close to Chinatown we stumbled across a vegan dessert stall. They had waffles, doughnutty cake things, and chocolate cake. We bought one of everything.

Kusum Indian

All vegetarian, thali and chapati seem to be vegan, though the dessert that comes as part of the dinner set (ice cream) is not. Declined that, but paid the full price anyway. The thali was three curries, rice and chapati, and they were delicious and homecooked. There was no menu, we just sat down and the owner brought out dish after dish. The samosas were great, I could have eaten them all night. Good job I didn't though, or I wouldn't have had room for the curries. As it was, I took some leftovers home. Food all cooked by the owner and his wife, though they seemed kind of despondent. There wasn't anyone else there when we were, early evening.

Difficult to find, the map marker in HappyCow was about 15 minutes too far west. But some googling for the name and different parts of the address eventually got us there. We almost walked right past, but I was lucky to see the sign fro the Indian supplies store that is right below the restaurant.

Food in Osaka

atl

All vegan, located upstairs, just off the side of the enormous indoor mall arcade thing that runs through the center of the city. Their specialty for some reason is bagels and hummus, which are made fresh onsite every day. They have three set lunches, which include starters and drinks, and three dessert options for a little extra. It was all really good, filling.. felt expensive, but actually normal for vegan restaurants here.

Mel Coffee roasters

Friendly, young, husband-and-wife team running this teeny tiny coffee roasters which has been carved out of a corner of a building. They have a bench outside, but no real seating. Any space inside not taken up by the counter is occupied by coffee roasting equipment, and you can watch the beans go round.

Seriously good espresso, and a wide selection of hand-drip, too. Plus, the cheapest coffee we found between Kobe and Osaka at 190 JPY for an espresso! And by far the best. Did I mention it was great?

Their English is fluent, and as an added bonus had a good working knowledge of vegan restaurants in the area.

Wad

This is a tea (and cereamics) shop, recommended to us by the folks at Mel's. We tried two different types of sencha, which was produced with great ceremony. It was very pretty, with teeny tiny cups, pots and timers. We initially tried to share a pot (it's expensive!!), but we were required to make an order each. We got three infusions, at different temperatures, and finally - the part we'd been excited about after reading it on the menu - they brought us the tea leaves to eat. Except they returned them seasoned with soy sauce and bonito flakes. D'oh.

They have a bunch of tea-appropriate nibbles on the menu, many of which look vegan, but I didn't try any.

They sell a very small selection of tea to buy by the gram as well.

Paprika Shokudo

All vegan and proud. They used a button system to call servers, but it was chronically slow anyway, including the food coming. In the end it took so long we decided not to get dessert.

But the food we did get was great. 'Oysters' made from mushrooms, fried soy meat, and cheesey vegetables. They also brought us some small starters to choose from a plate.

Prana

All vegan, macrobiotic, healthy food. There's a kitchen right across the street from the actual restaurant which was at first confusing.

No English menus, but the server/chef did her best to explain what the dishes were. We picked two out of the three lunch sets at random, and tried miso soup, salad, curry, and ramen. The ramen were bland but a large portion. The curry was on par with other curries we've had a vegan restaurants. We followed up with two (small) slices of apple cake. The food was all good, but definitely on the more expensive side.

Aju

This place. Wow.

All vegan, and proud.

Reviews on HappyCow claim it only has four seats, and a grumpy owner/chef, but I found a much bigger space and a cheerful, curious, talkative waitress. Their space was occupied by a prebooked large party, but they managed to dig up some extra chairs and repurpose a storage table so that we could stay!

Not on the cheap side, but we ordered as much as possible. I finally got to try oknomiyaki which was maybe one of the most delicious things I've ever eaten. Plus a pizza with something spam-like, and potato. It was so cheesy and absolute comfort food. We also tried deep fried soya meat, which came topped with more grated radish than one should reasonably try to eat. We got a platter of sides, including bizarre 'squid' (which I was reliably informed had a texture very close to actual squid), and soy meat chunks, and various salad-y bits.

There was a poster on the wall with a picture of some ridiculous looking Hallowe'en dessert, and I had to have it. It was pumpkin soft-serve ice cream, matcha ice cream, red bean goo and mochi balls. Plus little biscuits shaped like a bat and a pumpkin. I regret nothing.

This was my last night in Osaka, and I was tempted to stay longer just to come back here.

Accommodation in Osaka

I stayed in a small self-contained apartment near Tennoji. It had a balcony, and a small but functional kitchen. It also came with a portable Mifi hotspot which was fast and the most useful thing ever.

Also posted to AirBnB:

Great communication from Keisuke right up until I arrived. Really great place, clean and minimal and comfortable. Also a good location, for a train to the airport, and for central Osaka. In fact, I walked into Osaka; it takes more than an hour but is a great way to see different areas. The apartment is also close to a large park and many tourist attractions, including Tsūtenkaku tower. Thanks!