216 pages.
79,165 words.
4 years and 7 months and 2 days
21 countries.
216 pages.
79,165 words.
4 years and 7 months and 2 days
21 countries.
This looks quite heavy.
My thesis is, and always has been, online at dr.amy.gy. You can read it, and you can even annotate it with dokieli, or open github issues, so long as you acknowledge that I rushed a lot of parts (my own fault). I will continue to improve it over the coming months, and my defense/viva will be in September, after which I expect lots of corrections and to republish a better version. So don't feel bad if you want to wait until then to read it :)
Now I am literally going to meditate on a hill in Malaysia for ten days. Ciao.
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A few days in Penang. One night in a capsule hotel (covered by the hostel that double-booked me) and then a few days being fed and looked after by Tammy and Jon of Wholey Wonder whilst I desperately finished my thesis. A trip to Chew Jetty and the underwhelming Crystal Museum. Breakfast with Malaysian Mum at Purple Stone in Air Itam before heading up the hill to meditate.
I am back online, but I don't really want to be.
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Some photos from the Vipassana meditation center on Penang Hill East, with a view over Air Itam and Kek Lok Si temple. I took them on the last day, when I got my phone back. Then I hauled a number of co-meditators to Wholey Wonder and chilled out there for the rest of the day. Many people had spent the last ten days silently contemplating my dreads (particularly the people who sat behind me in the meditation hall and dining hall), and a few concluded they wanted some of their own.
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One night and a morning in KL. Three hours in a bed-bugged bunk in an otherwise nice hostel. I meditated on the rooftop, and met a cool Syrian guy who advised me where to get breakfast.
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One day in Tokyo with Dave and J, who looked after me in shifts as they were never both free at the same time. I did Dave's laundry and made him eat vegetables for lunch. J made me a super romantic dinner, with candles and light jazz. She homemade vegan spaghetti bolognese, chocolate cake, and coconut ice cream! It was incredible. I gave her a dress I picked up in Egypt a few years ago and haven't been wearing much. Then I flew to Moscow.
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A brief stop near Mestre in Venice, some vegan food in a bookstore cafe, then the train to Trieste.
In reply to:
I like how this article seeks to accommodate a broad view of viable data sources for research, and particularly encourages data sharing and reuse between researchers.
The authors provide three examples of existing tools which could do (or be adapted to do) parts of the suggested pipeline. I hope that publishing this encourages others who are developing tools along these lines to come forward and let the authors and others know so that the community can start a comprehensive directory, as I'm sure there are plenty more.
It would be helpful to also have a characterisation of what is definitely missing as far as the authors know, and what the authors think are good directions to priortise for near term research and development.
Obviously I agree with the authors' call to open source such tooling for community benefit. I'd be particularly interested to hear your thoughts on the "agreed-upon integration platform" and what you think the best forum for discussing such a platform would be. Hopefully we can come up with ideas for that during the EDSC workshop discussion sessions!
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Eating and wandering around Trieste.
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More food, more wandering, Trieste.
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Grotto Gigante, walk to Miramare, Castello di Miramare, and the seafront
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An hour walk to get vegan pizza at Le Agavi
I spent the first few days wandering around the center of Trieste, and easily stumbled upon all of the Piazzi (I'm going to assume this is the plural of Piazza without looking it up), piers, statues and Roman ruins that todo-in-trieste guides tell you to see. The core of Trieste is small and compact, as well as alive and beautiful, day and night. The town is set into the base - and creeping up the side - of hills which turn to mountains. From any perspective the backdrop is stunning. Green mountains dotted with orange rooftops in one direction, and the bright blue Adriatic Sea in the other.
More photos from wanderings here and here.
You probably know you can't confine me to a new town's core for very long though. Yesterday we took the 42 bus to Grotto Gigante, a giant cave about a 30 minute ride up and over some hills out of Trieste. Well worth the 9 EUR entrance fee (for student; 12 for 'adult'), this enormous chasm is one of the largest publicly accessible caves in Europe. Guided tours are hourly, and we learnt about the history of the cave's discovery and usage, the growth of the stalagmites and stalagtites, and the scientific research that goes on down there. Our tourgroup was occupied by an enormous pack of schoolkids, but the guide did a great job at distracting them so we (the handful of non-Italian speakers) could take undisturbed photos, and keeping them quiet whilst she recapped the information in English.
The cave really is enormous, and the rock formations are really cool. It took about an hour to tour through it. The temperature inside is a cool 11 degrees C, and damp.
The tickets included a 10% discount at the nearest restaurant, but the staff there were surly and none of the food looked good. There was nowhere to buy a bus ticket around the Grotto Gigante, so I figured we could walk along the bus route a bit and somewhere would surely pop up in one of the villages. Bus tickets here are bought before boarding, from corner shops or (less available) ticket machines. Nowhere popped up. Kit was a good sport and agreed to walk all the way to Miramare though (GPS trace). Some of this route was along roads, but OpenStreetMaps showed plenty of off-road trails which we took when we could. It was a very pleasant walk through grassy woods in between small villages, and all downhill.
We reached Miramare after one and a half hours. Castello Miramare is a stately home standing over the sea, and set in an enormous and impressive park grounds. We stopped for lunch at the cafe in the park, which was nice. I had a perfectly adequate roasted vegetable panino, and Kit ate lasagne and claims he has definitely made better ones himself. The surroundings were lovely though.
I went to check out the castle, but it's a new one not old, and inside was art galleries and furniture. I felt I could spend the 8 EUR entrance fee on something I'd enjoy more. I did find out from the friendly staff in the ticket office that there is nowhere within 5km to buy a bus ticket though, and the best option was just to hop on the bus and plead ignorance if we were asked for a ticket.
We followed the coast around to the park exit, and then along a bit more to the bus stop. The coast between Miramare Trieste for a few km is concrete 'beach' Barcolo with steps leading directly the the ocean. It was well populated with sunbathers and swimmers. Trieste doesn't have any sand beaches, but actually that's far more practical. It doesn't seem to make any difference to the locals.
We took the number 6 bus back to town. It was packed, and our lack of ticket went unnoticed. More photos from the cave, castle and walk between them here.
Kit was done with walking, but after a couple of hours back at the hotel I had itchy feet again. I took the opportunity to quest for vegan mozzerella, at a pizzaria I found on HappyCow, one hour's walk from Trieste center. Walking through Trieste though is never a waste of time, even without vegan cheese at the end of it. OpenStreetMap routed me through some wonderful winding streets, and then along a cyclepath. This cyclepath was sheltered from the city center, and turns out to be 12km long and leads to Slovenia. Awesome. (GPS trace).
Le Agavi did not disappoint. It's far enough away I'm not sure if it's even technically in Trieste, but it was on a quiet street with indoor and outdoor seating. A vegan menu with several options; rice-based mozzerella, tofu, various sauces and veggies, I was spoilt for choice. I devoured one pizza, then ordered two more to takeaway because I'm an adult and I can do whatever I want. I took the bus back to Trieste center. Photos from the walk and eating.
This morning I had pizza for breakfast, then set out to check out Castello San Giusto. A student entrance is only 2 EUR; it has an armoury, some historical rooms, and walls with, you guessed it, specatcular views in all directions.
On the way I stopped for chocolate cherry gelato from Gelato Marco. Now I'm in Zoe Market, an all vegetarian cafe and store, which has lots of vegan options and milks. There's no wifi, but there's one power outlet, and it's a nice place to sit and catch up on blog posts..
I've been in Italy less than a week and I already have a pizza backlog.
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Castello San Guisto in the center of Trieste, featuring gelato from Gelato Marco and lunch at Zoe Market.
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The port, Pedocin, pizza
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Molo Audace and views from Ostello Tergesto
After drafting my last post from Zoe Market cafe, I was struck with the urge to see what the Trieste coastline had to offer further south. I walked to the port area, and discovered it's not really a place for wandering.. big highways and industrial buildings. Nonetheless, even the warehouses and apartment blocks were fairly aesthetically pleasing, and at one point a long park runs parallel to the coast, almost like an apology. GPS trace of the walk here.
I did make it to Pedocin beach eventually though. It took a while to find.. I walked around the pier, which felt quite dead, and found the lighthouse. But industrial buildings in every direction seemed to be preventing me from accessing the coast.. though as I walked past one large wall, I could hear children, so I persisted. Eventually I found the entrance, through an unassuming concrete cabin. I think the entry fee is 1 Euro, but there was no-one there to take it. The cabin has two exits, on the left for women and the right for men. A wall divides the beach in two. The beach is pebbles, with immediate access to the sea; small and peaceful, with one vendor selling drinks and snacks. I napped until I was woken by the tide lapping at my feet.
Super pretty white and purple barrel jellyfish fill the bay around here, and Pedocin was no exception. It was only 20 minutes to follow the coast around back into town. More photos here.
In the evening I ate cake from Giardina Tergesteo and pizza (oops) from DNapoli. I had to add the remaining half of a Marinara to the pizza I had already accumulated from Le Agavi the day before.
The next day we picked up gelato and took that and the pizza backlog to Molo Audace, a long concrete pier off Piazza Unita, for a picnic. Later in the evening I walked by myself to ErbOsteria, a charming vegetarian restaurant which uses aromatic herbs for all dishes. I was the only one there for most of the evening, and was treated to a three-course vegan meal with homemade iced tea. It was a wonderful change from the white-flour-and-tomato based meals I've been eating most of the week; high quality ingrediants, freshly crafted, and I was ready to pay gourmet prices. There was no written menu as it changes daily, so I had no idea what to expect to pay.. and three courses plus tea plus an extra dessert to take back for Kit came to 13.50EUR! Unbelievable. My phone was dead so I only managed to take crappy pictures of the food with my laptop webcam. I'll spare you. The starter was fresh courgette, thinly sliced and raw, dressed with lemon and mint. The main was gnocchi (boiled potato dumplings) with asparagus sauce (I heard the blender go, so I think the asparagus was freshly sauce-d for me) sprinkled with almonds. Followed by cake with balsamic herbs. I took a slice of stunning strawberry tart back for Kit, as I don't like strawberries but it looked far too good to go to not be appreciated by someone. He'd eaten it before I remembered to take a photo.
As of this morning, I relocated from Trieste center to a hostel up the coast, near to Miramare. It is directly on the seafront.. this is the view from the balcony, where I'm typing right now. Soon I will be bored of typing, and will go down to enjoy the last few hours of sun from that concrete beach I told you about in my last post, and hopefully find some granita.
Trieste is small, so as you'd expect pure veg*n restaurants are limited. There was nonetheless more than enough to keep me occupied for a week though. Of course, every Italian restaurant offers the chance to take vegetarian pizza and pasta dishes without cheese, and most offer pizza marinara and spaghetti pomodoro anyway if you don't feel like making special requests.
Giardinio Tergesteo: a vegetarian restaurant with a lot of vegan options that I returned to over and over. They have ample seating options outside, inside, and outside-inside in a kind of mall area. There's power and wifi, and it's the sort of place you could go for a formal dinner, or to spend an afternoon with your laptop. At lunchtimes on weekdays they have a changing pasta dish, and the rest of the time they have salads, sandwiches (various breads and fillings) and a variety of vegan cake.
Erb Osteria: somewhat out of the way and in an odd part of town, this is a small vegetarian restaurant where all dishes are oriented around aromatic herbs. The menu changes daily, so it isn't written down. The decor was very cute, and it wasn't busy when I was there early evening. I asked the owner to furnish me with courses of vegan dishes, and was not disappointed. I was even more surprised by the price at the end, which was 13 EUR for a starter, main, dessert, iced tea, and another dessert to go. You would have to go out of your way to pass here I think, but worth a detour.
Draw Food: Draw is raw, but not all vegan. The menu is mostly meat and fish options, but one section is veg*n and some dishes can be tweaked to remove non-vegan cheese. They have their own cashew-based ricotta which I couldn't get enough of. There's power and wifi, and the decor is great. I spent an afternoon here with my laptop, as well as returning for several other meals, lunchtime and evenings. I had the aubergine ricotta dish twice, and it was slightly different but deliciously creamy both times. I also tried courgette spaghetti with mushrooms, which had an interesting tomato sauce, and a wrap. The dishes are beautifully presented, and small but well crafted. From here I also had juices, milkshakes, and coffees, when soya milk was available.
Genuino: is a good-for-you 'fast' food outlet, and everything comes packaged to-go, though there's plenty of space to eat in. The menu is omnivorous, but I tried all the vegan options I think: the vegan burger (a vegetable patty with copious salad, roasted potatoes, in a panini), a wild rice dish with finely chopped veggies, nuts and seeds, and a rich tomatoey sauce, and something similar but with millet.
La Caveja: is on the same lines as Geniuno, but with wraps. They have a separate vegan menu, which includes a hazelnut chocolate dessert wrap. Meanwhile, I tried roasted vegetables with a really delicious harissa sauce.
Gelato Marco: is a well known gelateria which has around a dozen vegan flavours. I worked my way through, trying chocolate cherry, different combinations of fruit sorbets, hazelnut, pistachio, and others..
Le Agavi: is a pizza place on the outskirts of Trieste; I walked an hour from the center to reach it. They have a big vegan menu, of pizzas topped with rice mozzerella and combinaions of tofu and vegetables, as well as different sauces. For some reason, leeks feature heavily. Totally worth the walk; I ate one there and took two back.. more in this post.
At D'Napoli (famous for pizza), they tweaked the gnocchi for me to remove mozzerella and add chilli (most places don't have chilli so this was great). The spaghetti pomodoro I had at a few places on various occasions, ever simple, was consistently rich and delicious. Aside from just wanting greens in my diet, I didn't tire of the experience of consuming this dish.
In reply to:
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.
In reply to:
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 :)
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Final evening in Trieste
In reply to:
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.
Hate the state of academic publishing? Love it? Somewhere in between? Come to Enabling Decentralised Scholarly Communication workshop in room Aurora 1 at 9 tomorrow!
Okay I'm burnt out on small talk after the first coffeebreak. If anyone wants to just stand together without conversing so as not to look lonely/lost I'm game.
Elsevier keeps 'ghost profiles' for people who don't have Mendeley accounts. You can "claim" your ghost, and it's "yours".. but uh.. not really because it's centralised. And this is presented like a nice fun helpful thing. Ghost profiles is some facebook-level creepy surveillence profiling shit. Makes me sad :( But not surprised.
It was only a matter of time. Lightning talk by csarven about Linked Data Notifications.
ESWC is fun and all but when is it time to go in the sea?
Starting in ten minutes - Enabling Decentralised Scholarly Communication. Live notes on etherpad.
(Room Aurora I)
"...if our scholarly infrastructure is no longer fit for purpose, can we use it to change itself?"
Dave de Roure asks the hard questions, talking about Scholarly Social Machines at EDSC2017.
Great discussion at Enabling Decentralised Scholarly Communication on the topic "what did third-party publishers ever do for us?" Notes so far on etherpad.
At 12, csarven will present Linked Data Notifications.. Come to the talk for an overview, then if you want to integrate a part of the protocol into your existing applications, or build a receiver from scratch, we're both here all week and ready to help!
csarven presents Linked Data Notifications at ESWC2017... Starting with some motivational use cases in the social web space to which this W3C Recommendation has been applied so far.
LDN is based on Linked Data principles, enables decentralisation, and persistence of data.
LDN questions from the audience...
About reference implementations... The test suite automatically checks compliance, and most implementations are open source.
From people who are already considering to include LDN in their projects, asking for technical tips.
Authentication/login part... this isn't part of the protocol, orthogonal.
About LDP and Web of Things... can devices send notifications? What if applications can't use JSON-LD? Well, that's part of the Rec that applications must be able to at least do JSON-LD, but to cooperating applications can use content negotiation to agree on a more lightweight RDF format if they want. It's important for interoperability to be able to send JSON-LD in case a receiver can't understand any other RDF syntaxes; but if your sender and receiver both agree on another format (via the Accept-Post header) they can use that.
Do additions to the simple protocol make it complicated? What about spam? LDN recommends application-specific constraints to deal with issues like this. We don't have a blanket suggestion for how to deal with these kinds of problems in every domain though, we leave it to more focused experts.