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945 results for “bridgedb”
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BridgeDb Java 3.0.30 is released: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.30 https://doi.org/10.5281/zenodo.18157075
"This release updates to BridgeDb Datasources 20260105 adding a few hundred more species and updates various dependencies and Maven plugins."
BridgeDb Java is the library that implements a Java API to access identifier mappings (e.g. from #ChEBI to #Wikidata, or from Ensembl to UniProt) from local files.
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BridgeDb Java 3.0.29 is released: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.29
"This update release brings in BridgeDb Datasources 20270728, improves the backwards compatibility with old Apache Derby versions, adds a BridgeDb.getVersion() method, and updates various dependencies."
BridgeDb Java is the library that implements a Java API to access identifier mappings (e.g. from #ChEBI to #Wikidata, or from Ensembl to UniProt) from local files.
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BridgeDb Java 3.0.27 is released: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.27
"This update release brings in BridgeDb Datasources 20240725, a new organism (Solanum tuberosum), and various small stability improvements."
BridgeDb Java is the library that implements a Java API to access identifier mappings (e.g. from #ChEBI to #Wikidata, or from Ensembl to UniProt) from local files (there is API support for online services too, but we need help maintaining this code).
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BridgeDb was mentioned today at the #DataReuseDay2024 in Leiden as important solution to integration databases with different identifiers for the same things
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@torproject Not to mention it being used in more and more #Cyberfacist regimes to preemptively detain and harrass and detain people without charges.
And yes, that also happens in the global "west"...
https://mstdn.social/@kkarhan/110533134513076980So let the #Wumao at least work for their sweet entries manually farming #BridgeDB @ https://bridges.torproject.org aka.
http://yq5jjvr7drkjrelzhut7kgclfuro65jjlivyzfmxiq2kyv5lickrl4qd.onion for #TorBridges... -
@torproject Not to mention it being used in more and more #Cyberfacist regimes to preemptively detain and harrass and detain people without charges.
And yes, that also happens in the global "west"...
https://mstdn.social/@kkarhan/110533134513076980So let the #Wumao at least work for their sweet entries manually farming #BridgeDB @ https://bridges.torproject.org aka.
http://yq5jjvr7drkjrelzhut7kgclfuro65jjlivyzfmxiq2kyv5lickrl4qd.onion for #TorBridges... -
Making new connections: from BridgeDB to Rdsys
Telegraph (telegra.ph/Making-new-connecti…)
blog.torproject.org/making-con… -
meanwhile, one @bridgedb feature request implemented: the website now also lists the species common names (if giving on the JSON config files)
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bringing together a few Dutch #openscience projects at #NOSF2025
We see the Dutch VHP4Safety project, @bridgedb, @elixir_europe TeSS, and the @SURF https://taxila.nl/
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@[email protected] almost there... meanwhile, making a @bridgedb Java 3.1.14 release for PathVisio, the tool we use to make digital biological pathways in @wikipathways
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Project #7: fixed a big, had a meeting with @bridgedb, worked on Rhea, and Bgee. They're still looking for more databases to integrate. (Check out https://togoid.dbcls.jp/ !) Btw, "Togo = integration in Japanese" (from the slide)
Project #8: Developing a lesson for the ELIXIR Software Management Plan.
Project #9: FAIR comp models via BioModels. Curated 3 ML models and identified issues. Automated extraction of metadata to server "F"-indable. Using ONNX
#BioHackEU22 4/
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I am attending (online) the #RCIM #ELIXIRMetabolomics #MetabolomicsCommunity #RCI kickoff meeting. @tgx_um has a role in this @elixir_europe Science Tier grant related to semantic technologies (links to @bridgedb and @wikipathways, etc) and outreach (FAIR Cookbook, OER)
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in collaboration with MaCSBio we today start the first #EpiLipidNET training school on Data Analysis Techniques for preprocessed Lipidomics data. This includes the #openscience @wikipathways and @bridgedb projects. See this earlier post: https://social.edu.nl/@bigcat_UM/112024997890956725
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@torproject Not to mention it being used in more and more #Cyberfacist regimes to preemptively detain and harrass and detain people without charges.
And yes, that also happens in the global "west"...
https://mstdn.social/@kkarhan/110533134513076980So let the #Wumao at least work for their sweet entries manually farming #BridgeDB @ https://bridges.torproject.org aka.
http://yq5jjvr7drkjrelzhut7kgclfuro65jjlivyzfmxiq2kyv5lickrl4qd.onion for #TorBridges... -
I am attending the 4th #EpiLipidNET meeting in Toulouse tomorrow and Wednesday. Tomorrow I will demo @wikipathways @bridgedb and #pathvisio and on Wednesday I get to show some of the new things in these projects. I will cover the meeting from this account
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Avalanche Sees Surge in BTC Bridged to Its Network With Over $44 Million in Bitcoin Ported on Thursday - According to statistics, the number of bitcoin bridged to the Avalanche blockchain... - https://news.bitcoin.com/avalanche-sees-surge-in-btc-bridged-to-its-network-with-over-44-million-in-bitcoin-ported-on-thursday/ #decentralizedfinance #lightningnetwork #digitalcurrency #uniqueaddresses #virtualcurrency #bridgedbitcoin #cryptocurrency #publicchannels #duneanalytics #onchaindata #news
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Avalanche Sees Surge in BTC Bridged to Its Network With Over $44 Million in Bitcoin Ported on Thursday
https://news.bitcoin.com/avalanche-sees-surge-in-btc-bridged-to-its-network-with-over-44-million-in-bitcoin-ported-on-thursday/
#decentralizedfinance #lightningnetwork #DigitalCurrency #Uniqueaddresses #VirtualCurrency #bridgedBitcoin #Cryptocurrency #publicchannels #DuneAnalytics #Onchaindata #Blockchain #investment #Avalanche #protocol #transfer #Bitcoin #Bridges #Finance #network -
Avalanche Sees Surge in BTC Bridged to Its Network With Over $44 Million in Bitcoin Ported on Thursday
https://news.bitcoin.com/avalanche-sees-surge-in-btc-bridged-to-its-network-with-over-44-million-in-bitcoin-ported-on-thursday/
#decentralizedfinance #lightningnetwork #DigitalCurrency #Uniqueaddresses #VirtualCurrency #bridgedBitcoin #Cryptocurrency #publicchannels #DuneAnalytics #Onchaindata #Blockchain #investment #Avalanche #protocol #transfer #Bitcoin #Bridges #Finance #network -
Avalanche Sees Surge in BTC Bridged to Its Network With Over $44 Million in Bitcoin Ported on Thursday - According to statistics, the number of bitcoin bridged to the Avalanche blockchain... - https://news.bitcoin.com/avalanche-sees-surge-in-btc-bridged-to-its-network-with-over-44-million-in-bitcoin-ported-on-thursday/ #decentralizedfinance #lightningnetwork #digitalcurrency #uniqueaddresses #virtualcurrency #bridgedbitcoin #cryptocurrency #publicchannels #duneanalytics #onchaindata #news
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Avalanche Sees Surge in BTC Bridged to Its Network With Over $44 Million in Bitcoin Ported on Thursday - According to statistics, the number of bitcoin bridged to the Avalanche blockchain... - https://news.bitcoin.com/avalanche-sees-surge-in-btc-bridged-to-its-network-with-over-44-million-in-bitcoin-ported-on-thursday/ #decentralizedfinance #lightningnetwork #digitalcurrency #uniqueaddresses #virtualcurrency #bridgedbitcoin #cryptocurrency #publicchannels #duneanalytics #onchaindata #news
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Avalanche Sees Surge in BTC Bridged to Its Network With Over $44 Million in Bitcoin Ported on Thursday - According to statistics, the number of bitcoin bridged to the Avalanche blockchain... - https://news.bitcoin.com/avalanche-sees-surge-in-btc-bridged-to-its-network-with-over-44-million-in-bitcoin-ported-on-thursday/ #decentralizedfinance #lightningnetwork #digitalcurrency #uniqueaddresses #virtualcurrency #bridgedbitcoin #cryptocurrency #publicchannels #duneanalytics #onchaindata #news
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Project #5: one of the projects about #bioschemas, this one about the Data Discovery Engine
Project #6: pipeline project, I think, about genome reconstruction. Galaxy, of course
Project#7: FAIR data, with TogoID, MetaStanza. (Need to talk with them, I guess, about @bridgedb and perhaps SSSOM)
#BioHackEU22 3/
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if you wonder why #epilipidnet WG4 was missing, that's the WG where we're involved. Florian Gruber (the chair) presented some recent work on lipids in our skins and how cholesterol modulates restructuring of the membranes and the tissue structure. I (co-chair) presented the @wikipathways work (tho I see I should not have left out the @bridgedb slide) and the state of the #lipids portal (https://lipids.wikipathways.org/).
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use descriptions on how chemists identify chemical structures: https://aionics.io/blog/why-chemical-identifiers-are-the-unsung-heroes-of-innovation/
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Many of my neighbors do not have running water in their homes as the shut off relief runs out and families inherit old houses with systems in need of repair. Detroit meanwhile has high rates as we subsidize the suburbs.
“For the past 25 years, Detroiters have borne the bulk of stormwater upgrades – a capital program that has exceeded $1.5 billion.
The approximately 680,000 residents of Detroit have borne these costs despite accounting for only 23% of GLWA’s 2.9 million wastewater customers.”
https://mastodon.social/@bridgedet313/116572345245498725 -
The thread about #NowAndThen photo montages of old railway stations, tramways and bridges around Edinburgh and Leith
This thread was originally written and published in December 2017 and a further part in May 2019.
This thread features #NowAndThen photo-montages of long gone railway stations, tramways and bridges in Edinburgh and Lieth; period photos overlaid on the current streetscape to show just how much or little things have changed over time.
Duke Street in 1954 on the last day of service for the No. 25 tram. This service ran from Corstorphine to Portobello King’s Road via Leith Walk and the Links. Not much else has changed on this side of the road, although the occupants of the buildings certainly have. On the left was the Palace Cinema, with a snooker hall above. It is now a J. D. Wetherspoon pub.
No. 25 Tram at Duke Street. Original image © Kenneth G. WilliamsonCommercial Street in 1955. The No. 17 tram from Granton passes the “Highland Queen” bonded warehouse of MacDonald and Muir. It is running across the railway lines that crossed into the docks from the former North British railway at North Leith / Leith Citadel station. The bond is now flats, through the West Dock Gate where the railway ran is the now the Scottish Government building – Victoria Quay. The Old West and East docks are infilled, unimaginatively used as car parks. The Victoria Dock is cut off from the harbour basin and is a sterile and bleak water feature in front of Victoria Quay.
No. 17 tram at Commercial Street. Original image © Kenneth G. WilliamsonKing’s Road at Portobello in the 1950s. The No. 12 tram from Corstorphine via Leith, it has just passed the ghost of a car heading the other way to Portobello. The background is dominated by the great red brick lump of Ebenenzer J. Macrae’s Corporation electric power station.
No. 12 Tram at the King’s Road. Original image © Kenneth G. WilliamsonTollcross in 1956. There was a tramway depot here – where the central fire station now is – and the route was also a junction where 3 routes from the suburbs converged and then split immediately into two to head into the city by different routes. As such this was always a busy place on the network and this scene is busy with shoppers and tramcars. The tenement on the right and the castle are all that remain of the original buildings in this shot now.
Trams at Tollcross. Original image © Kenneth G. WilliamsonTrinity Crescent in the 1950s. A no. 17 tram squeezes under the bridge carrying the railway from Trinity Station along Lower Granton Road to the docks. The low bridge and tight S-shaped turn of the road meant that the tramway here was single line in the middle of the road, with the overhead line lowered. A set of traffic signals allowed only 1 tram at a time into this short section and warned motor vehicles that a tram was about to pass as their route swung onto the right lane to make the turn.
No. 17 at Trinity Crescent.And Trinity again in 1986. A ghost train crosses Trinity Road on track removal duties. Click on the link to the EdinPhoto website to see more images of this series.
Trinity railway bridge in the 1980s. Original photo © Peter Stubbs.Moving on to animated transitions, here is Balgreen Halt station. A 1934 addition to the suburban railway network by the LNER (London & North Eastern Railway), it was closed in 1968. Estimate the old photo is early 1960s.
Balgreen Halt. Original CC-BY-SA Ben BrooksbankAnd at the end of the line at Corstorphine. Always a hard one to get your head around as no hint of the stations presence is left under the 1980s housing, beyond the name “Station Road”
Corstorphine Station, 1926. Original Image © Edinburgh City LibrariesSide fact, Corstorphine had extraordinarily long platforms for a suburban station (250m, sufficient for a 12 coach train of 60 foot stock), I believe this was because the railway company hoped that a new barracks to replace the Georgian cavalry establishment at Piershill would be built nearby. The new barracks were ultimately built at Redford instead but Corstorphine was left with its overly large station. There were 2 full platforms and 2 full length carriage sidings. As a result it was used to stable and clean coaching stock overnight and on occasions such as rugby and football matchdays.
Another overlooked Edinburgh suburban station; the awkwardly located Piershill at the foot of Smokey Brae, between Meadowbank and Restalrig. The road here running under the bridge is Clockmill Road, which connected to the Clockmill Lane. This was the ancient route from the Canongate to Restalrig, cut in two by the London Road when it was built in the early 1820s. The road was obliterated and the bridge cut off by the groundworks for the 1970s Commonwealth Games stadium, the velodrome being built on top of the road. The bridge is now blocked up as a garage, but may be re-opened as a through route in the future when the eastern end of the stadium site is redeveloped as housing.
Piershill Station. Original Image © CanmoreLeith Walk station – no, not the big one at the Foot, but the one called Leith Walk towards the top.The demolished tenements of Shrub Hill and Shrub Place are in the background, plus an intriguing belfry. I’m guessing it was the old school next to Pilrig Model Buildings, which later became the “Royal Caledonian Bazaar”.
Leith Walk station, 1890s. Original from The Story of Leith by John RussellNow the site of the Inchkeith House multi-storey flats, the Royal Caledonian Bazaar was a “posting and livery establishment”; basically a horse transport depot. The proprietor was one John Croall. The Croalls were established in the horse business and were pioneers of motoring in Edinburgh. They gave their name, unsurprisingly, to Croall Place, the tenement at the top of Leith Walk where it meets Macdonald Road. Croall & Croall later built car and bus bodies and had a number of works around the West Port and Lothian Road. They later became part of the SMT (Scottish Motor Transport) empire.
Granton Road, once an important suburban commuter station and tram route. It was much more conveniently located for the wealthy suburb of Trinity than the station of that name, and later for the big new housing scheme at Boswall.
Granton Road station, 1955. Original image © Kenneth G. WilliamsonThere’s an old cast iron column just outside where the station was, I always assumed it was a tramway pole for the overhead wires. This photo shows it supported no wires – there’s an actual tramway pole right behind it – and it had a crown-shaped vent cap. It’s not a pole or a lamp post at all, it’s actually a sewer vent – a stink pipe – which is why it has survived.
We move on to Granton station itself. One of the first in Edinburgh and originally the site of a pioneering train ferry to Burntisland before the Forth was bridged. It closed in 1925 as an economy as there was little need by this time for a passenger station in the middle of the docks – most people taking the ferry across the Forth found the electric tramway much more convenient to get into the city than taking the train.
Granton Station, pre-1925. Original image © Kenneth G. WilliamsonThe slip for the train ferries is still used by the Royal Forth Yacht Club. Thomas Bouch’s Floating Railway was an ingenious and effective solution to bridging the Forth before the technology allowed a permanent structure. Basically an early, steam-raised linkspan that lowered a ramp on to a special ferry boat, allowing wagons and carriages to be run aboard. The whole apparatus, rails and all, was on a great wheeled carriage, allowing it to move with the tides. The rails were in short sections, bolted together in such a way that they could flex.
Bouch’s “floating railway”, a rather ingenious solution to the problem of bridging the Forth by railThomas Bouch is an engineer remembered for his greatest and most infamous creation, the first Tay Bridge, but he had a long career in which he constructed many pioneering and innovative solutions to the problems of getting railways across obstacles.
I’m quite chuffed with this image, which shows the evolution of the Upper Drawbridge at Sandport Place. Not only is the river much higher now since the docks were dammed, but the deck was widened and the central arch of the current bridge replaced the lifting section.
The “Upper Drawbridge” over the Water of Leith. Original Image © Peter StubbsThe Water of Leith is no longer a tidal river, as in the 1960s a set of lock gates were installed at the mouth of the docks to keep the dock basin always filled with water to allow bigger and deeper ships to use the port, and not be so restricted by the tides when coming and going. The water level these days is frequently within a foot of the central arch but you can still see the “river bed” in the right conditions only a few feet below that, there must be a good 20 foot of mud and silt and sludge built up on the river bed, unable to be washed out by the tide.
The next image is the same spot as before but looking the other way, to St. Ninian’s Wharf (named for the old North Leith Kirk behind, with its distinctive Dutch tower). The site of a dry dock and boatbuilding yard in the 1850s and 60s.
St. Ninian’s Wharf, original image by Thomas Vernon Begbie, taken in the 1850s. © Edinburgh City LibrariesThe photo confused me for a good while, as I assumed that the ship must be in the dry dock, which was one of the first dry dock in Scotland so pre-dated the photo by about 100 years. I later realised that the ship being built in the picture is not in the dry dock at all, but on a building slip alongside, with a temporary coffer dam following the line of the river wall – marked in red on the Town Plan below.
OS 1849 Town Plan. Reproduced with the permission of the National Library of ScotlandThat ship may even be on a “patent slip”, a Leith invention.
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#Lochend #Logan #Restalrig #StMargaret -
I sat under the stern of the ship where it bridged out like a fin shielding my head from the harsh rain.
I couldn't understand why the bay didn't have a roof, but I didn't mind. Until we came here I could not remember when the last time I was caught in rain.
"Pretty #grim huh?" I heard a voice behind me say.
"Grim... Nah. I grew up on one of the old mega ships... I never saw sky till I turned 17. I felt rain just 3 years ago."
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The #Telegram and #Matrix groups named #FamilyOfLisp are now synchronized (bridged):
🦎 https://telegram.me/FamilyOfLisp
🦎 https://matrix.to/#/#family-of-lisp:magdeburg.jetzt
The two groups are for friendly exchange and dialogue on topics related to the Family of #Lisp #programming languages.
🌺
🏷️ #Scheme #CommonLisp #Racket #Clojure #DylanLang #ELSConf #AMOP #CLOS #InterLisp #OpenGenera #LispMachine #Medley #ConnectionMachine #Symbolics #AutoLisp #MacLisp #ZetaLisp #EuLisp #ISLisp #CLHS #SICP #AIMA #CLtL2 #PAIP #HTDP
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The #Telegram and #Matrix groups named #FamilyOfLisp are now synchronized (bridged):
🦎 https://telegram.me/FamilyOfLisp
🦎 https://matrix.to/#/#family-of-lisp:magdeburg.jetzt
The two groups are for friendly exchange and dialogue on topics related to the Family of #Lisp #programming languages.
🌺
🏷️ #Scheme #CommonLisp #Racket #Clojure #DylanLang #ELSConf #AMOP #CLOS #InterLisp #OpenGenera #LispMachine #Medley #ConnectionMachine #Symbolics #AutoLisp #MacLisp #ZetaLisp #EuLisp #ISLisp #CLHS #SICP #AIMA #CLtL2 #PAIP #HTDP
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The #Telegram and #Matrix groups named #FamilyOfLisp are now synchronized (bridged):
🦎 https://telegram.me/FamilyOfLisp
🦎 https://matrix.to/#/#family-of-lisp:magdeburg.jetzt
The two groups are for friendly exchange and dialogue on topics related to the Family of #Lisp #programming languages.
🌺
🏷️ #Scheme #CommonLisp #Racket #Clojure #DylanLang #ELSConf #AMOP #CLOS #InterLisp #OpenGenera #LispMachine #Medley #ConnectionMachine #Symbolics #AutoLisp #MacLisp #ZetaLisp #EuLisp #ISLisp #CLHS #SICP #AIMA #CLtL2 #PAIP #HTDP