From 2673b681e47054aa96328798459d689d9237a596 Mon Sep 17 00:00:00 2001 From: Eduardo Pareja-Tobes Date: Sun, 15 Mar 2015 19:10:53 +0100 Subject: [PATCH 01/10] start with this --- .../2015-03-16-bio4j-a-roadmap.markdown | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 source/_posts/2015-03-16-bio4j-a-roadmap.markdown diff --git a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown new file mode 100644 index 0000000..ed22333 --- /dev/null +++ b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown @@ -0,0 +1,54 @@ +--- +layout: post +title: "Bio4j: a roadmap" +date: 2015-03-16 00:43 +comments: false +author: Eduardo Pareja-Tobes +categories: +- News +tag: +- news +- code +- roadmap +- future +- overview +--- + +## Bio4j: a roadmap + + +### new data integrated + +*ETA?* + +- ucsc human genome data, other genomic data +- reactome +- ... + +### Data release and distribution improvements + +*ETA?* + +- in-sync automated data import and releases +- improve usability from AWS +- standard data import brings easier in-house deployment tool + +### A Scala API + +*ETA?* + +- based on Scarph, the work of the nice guys at [oh no sequences!](http://ohnosequences.com). If you're working (or plan to) work with graphs in Scala, definitely keep an eye on this!! +- incredibly expressive super typed +- completely interoperability with the Java API in terms of data +- AWS deployment based on Statika + +### Angulillos improvements + +*ETA?* + +- use any Tinkerpop3 backend! use Bio4j with virtually _any_ graph db +- extend angulillos with more sophisticated combinators for traversals + +### Automated testing? + +*ETA?* \ No newline at end of file From 2e1368b7c17f7a5268e60207d26276b2c3c0196a Mon Sep 17 00:00:00 2001 From: Eduardo Pareja-Tobes Date: Mon, 16 Mar 2015 10:45:58 +0100 Subject: [PATCH 02/10] first cut at a list of new features / improvements --- .../2015-03-16-bio4j-a-roadmap.markdown | 46 ++++++++----------- 1 file changed, 19 insertions(+), 27 deletions(-) diff --git a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown index ed22333..0f27f47 100644 --- a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown +++ b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown @@ -14,41 +14,33 @@ tag: - overview --- -## Bio4j: a roadmap +# Bio4j: a roadmap +> The scope for this is: what's going to happen during 2015 in Bio4j. Right now this is just a list of points I want covered. Feel free to add / remove things, or comment in the commits if you prefer. +> +> **ETA**: Estimated time of arrival -### new data integrated +## New data -*ETA?* +- **ETA?** Human genome data, other genomic data. support for stabbing queries etc +- **ETA?** [Reactome](http://www.reactome.org/) -- ucsc human genome data, other genomic data -- reactome -- ... +## Scala API -### Data release and distribution improvements +- **ETA?** based on Scarph, the work of the nice guys at [oh no sequences!](http://ohnosequences.com). If you're working (or plan to) work with graphs in Scala, definitely keep an eye on this!! Incredibly expressive super typed. Complete interoperability with the Java API in terms of data +- **ETA?** AWS deployment based on [Statika](http://ohnosequences.com/statika) -*ETA?* +## Release and data distribution improvements -- in-sync automated data import and releases -- improve usability from AWS -- standard data import brings easier in-house deployment tool +- **ETA?** in-sync automated data import and releases, every 6 months. Predictable, stable, coherent, automated. +- **ETA?** small testing data subset based on SwissProt. + -### A Scala API +## Java API improvements -*ETA?* +- **ETA?** extend angulillos with more sophisticated combinators for traversals +- **ETA?** use any Tinkerpop3 backend! use Bio4j with virtually _any_ graph db -- based on Scarph, the work of the nice guys at [oh no sequences!](http://ohnosequences.com). If you're working (or plan to) work with graphs in Scala, definitely keep an eye on this!! -- incredibly expressive super typed -- completely interoperability with the Java API in terms of data -- AWS deployment based on Statika +## Documentation -### Angulillos improvements - -*ETA?* - -- use any Tinkerpop3 backend! use Bio4j with virtually _any_ graph db -- extend angulillos with more sophisticated combinators for traversals - -### Automated testing? - -*ETA?* \ No newline at end of file +- **ETA?** examples for every graph, model docs integrated with the source code \ No newline at end of file From 0cffefcf939fe4b8081b6942f2e214a251c80644 Mon Sep 17 00:00:00 2001 From: Pablo Pareja Tobes Date: Mon, 16 Mar 2015 11:10:38 +0100 Subject: [PATCH 03/10] Update 2015-03-16-bio4j-a-roadmap.markdown --- source/_posts/2015-03-16-bio4j-a-roadmap.markdown | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown index 0f27f47..2b587f8 100644 --- a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown +++ b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown @@ -43,4 +43,16 @@ tag: ## Documentation -- **ETA?** examples for every graph, model docs integrated with the source code \ No newline at end of file +- **ETA?** examples for every graph, model docs integrated with the source code + +## Dataviz + +In principle they would all be data visualizations that don't imply server requests. _(That doesn't mean that we won't be developing webapps in the future but we can first get a lot from what we already have without complicating things much more)_ We could include: + + - A few _dashboards_ built with [dc.js](http://dc-js.github.io/dc.js/) This kind of dataviz is quite nice to play with and people generally just love it _(even though they might not understand what's going on too much and they just click randomly at the charts to see what happens... :) )_ + - We should definitely have some sort of minimally interactive visualization of Bio4j data model, IMHO this is crucial not only for people that are willing to use Bio4j but also to get the big picture of what kind of data is included in the database. + - A set of biologically-wise interesting/useful visualizations _( @rtobes @marina-manrique @epareja @eparejatobes please some help here! ;) )_ + + ## Neo4j distribution + +I think this would be very important in order to regain some momentum for the project. The workload to get this running should not be much and, in turn, the benefits in terms of both visibility and potential engagements would be quite big. From 75f17598ccc41a1176054915ce2cbe4ea7308b96 Mon Sep 17 00:00:00 2001 From: Eduardo Pareja-Tobes Date: Tue, 17 Mar 2015 19:32:05 +0100 Subject: [PATCH 04/10] fix formatting, minor edits --- .../2015-03-16-bio4j-a-roadmap.markdown | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown index 2b587f8..3970a6e 100644 --- a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown +++ b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown @@ -41,18 +41,23 @@ tag: - **ETA?** extend angulillos with more sophisticated combinators for traversals - **ETA?** use any Tinkerpop3 backend! use Bio4j with virtually _any_ graph db +## Neo4j distribution + +- **ETA?** Finish the implementation of angulillos-neo4j +- **ETA?** write bio4j/bio4j-neo4j + +Is this actually valuable? If we develop a version of angulillos capable of wrapping any Tinkerpop3-compatible graph DB, we could use the tinkerpop3 version of Neo4j with that. + ## Documentation - **ETA?** examples for every graph, model docs integrated with the source code +- **ETA?** a paper; by the time this gets public we should already have a preprint -## Dataviz +## Datavis In principle they would all be data visualizations that don't imply server requests. _(That doesn't mean that we won't be developing webapps in the future but we can first get a lot from what we already have without complicating things much more)_ We could include: - - A few _dashboards_ built with [dc.js](http://dc-js.github.io/dc.js/) This kind of dataviz is quite nice to play with and people generally just love it _(even though they might not understand what's going on too much and they just click randomly at the charts to see what happens... :) )_ - - We should definitely have some sort of minimally interactive visualization of Bio4j data model, IMHO this is crucial not only for people that are willing to use Bio4j but also to get the big picture of what kind of data is included in the database. - - A set of biologically-wise interesting/useful visualizations _( @rtobes @marina-manrique @epareja @eparejatobes please some help here! ;) )_ +- A few _dashboards_ built with [dc.js](http://dc-js.github.io/dc.js/) This kind of dataviz is quite nice to play with and people generally just love it _(even though they might not understand what's going on too much and they just click randomly at the charts to see what happens... :) )_ +- We should definitely have some sort of minimally interactive visualization of Bio4j data model, IMHO this is crucial not only for people that are willing to use Bio4j but also to get the big picture of what kind of data is included in the database. +- A set of biologically-wise interesting/useful visualizations _( @rtobes @marina-manrique @epareja @eparejatobes please some help here! ;) )_ - ## Neo4j distribution - -I think this would be very important in order to regain some momentum for the project. The workload to get this running should not be much and, in turn, the benefits in terms of both visibility and potential engagements would be quite big. From 5479cb94d8e5577259afa14f1fac8620fc37e834 Mon Sep 17 00:00:00 2001 From: Eduardo Pareja-Tobes Date: Tue, 17 Mar 2015 19:45:41 +0100 Subject: [PATCH 05/10] add people per section --- .../2015-03-16-bio4j-a-roadmap.markdown | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown index 3970a6e..82318e8 100644 --- a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown +++ b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown @@ -19,30 +19,42 @@ tag: > The scope for this is: what's going to happen during 2015 in Bio4j. Right now this is just a list of points I want covered. Feel free to add / remove things, or comment in the commits if you prefer. > > **ETA**: Estimated time of arrival +> +> For each section there's a list of people involved, where the order is supposed to reflect the (decreasing) degree of involvement in that part. ## New data +**People** [@eparejatobes][@eparejatobes] [@rtobes][@rtobes] [@marina-manrique][@marina-manrique] [@epareja][@epareja] + - **ETA?** Human genome data, other genomic data. support for stabbing queries etc - **ETA?** [Reactome](http://www.reactome.org/) ## Scala API +**People** [@eparejatobes][@eparejatobes] [@laughedelic][@laughedelic] + - **ETA?** based on Scarph, the work of the nice guys at [oh no sequences!](http://ohnosequences.com). If you're working (or plan to) work with graphs in Scala, definitely keep an eye on this!! Incredibly expressive super typed. Complete interoperability with the Java API in terms of data - **ETA?** AWS deployment based on [Statika](http://ohnosequences.com/statika) ## Release and data distribution improvements +**People** [@laughedelic][@laughedelic] [@eparejatobes][@eparejatobes] [@pablopareja][@pablopareja] + - **ETA?** in-sync automated data import and releases, every 6 months. Predictable, stable, coherent, automated. - **ETA?** small testing data subset based on SwissProt. ## Java API improvements +**People** [@eparejatobes][@eparejatobes] [@laughedelic][@laughedelic] + - **ETA?** extend angulillos with more sophisticated combinators for traversals - **ETA?** use any Tinkerpop3 backend! use Bio4j with virtually _any_ graph db ## Neo4j distribution +**People** [@pablopareja][@pablopareja] [@eparejatobes][@eparejatobes] + - **ETA?** Finish the implementation of angulillos-neo4j - **ETA?** write bio4j/bio4j-neo4j @@ -50,14 +62,26 @@ Is this actually valuable? If we develop a version of angulillos capable of wrap ## Documentation +[@eparejatobes][@eparejatobes] [@rtobes][@rtobes] [@pablopareja][@pablopareja] [@marina-manrique][@marina-manrique] + - **ETA?** examples for every graph, model docs integrated with the source code - **ETA?** a paper; by the time this gets public we should already have a preprint ## Datavis +**People** [@pablopareja][@pablopareja] [@rtobes][@rtobes] [@epareja][@epareja] + In principle they would all be data visualizations that don't imply server requests. _(That doesn't mean that we won't be developing webapps in the future but we can first get a lot from what we already have without complicating things much more)_ We could include: - A few _dashboards_ built with [dc.js](http://dc-js.github.io/dc.js/) This kind of dataviz is quite nice to play with and people generally just love it _(even though they might not understand what's going on too much and they just click randomly at the charts to see what happens... :) )_ - We should definitely have some sort of minimally interactive visualization of Bio4j data model, IMHO this is crucial not only for people that are willing to use Bio4j but also to get the big picture of what kind of data is included in the database. - A set of biologically-wise interesting/useful visualizations _( @rtobes @marina-manrique @epareja @eparejatobes please some help here! ;) )_ + + +[@eparejatobes]: https://github.com/eparejatobes +[@pablopareja]: https://github.com/pablopareja +[@laughedelic]: https://github.com/laughedelic +[@rtobes]: https://github.com/rtobes +[@marina-manrique]: https://github.com/marina-manrique +[@epareja]: https://github.com/epareja From c97737b49df05f0e14efa9245a7d0c3d155b126d Mon Sep 17 00:00:00 2001 From: Eduardo Pareja-Tobes Date: Tue, 17 Mar 2015 20:11:52 +0100 Subject: [PATCH 06/10] fix formatting --- source/_posts/2015-03-16-bio4j-a-roadmap.markdown | 1 + 1 file changed, 1 insertion(+) diff --git a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown index 82318e8..b38fdfa 100644 --- a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown +++ b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown @@ -42,6 +42,7 @@ tag: - **ETA?** in-sync automated data import and releases, every 6 months. Predictable, stable, coherent, automated. - **ETA?** small testing data subset based on SwissProt. + ## Java API improvements From 841b5754664e0d184d5f063bda276219b2401584 Mon Sep 17 00:00:00 2001 From: Eduardo Pareja-Tobes Date: Wed, 18 Mar 2015 10:59:47 +0100 Subject: [PATCH 07/10] start adding dates, and more details about each section --- .../2015-03-16-bio4j-a-roadmap.markdown | 62 +++++++++---------- 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown index b38fdfa..b1a296a 100644 --- a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown +++ b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown @@ -24,60 +24,56 @@ tag: ## New data -**People** [@eparejatobes][@eparejatobes] [@rtobes][@rtobes] [@marina-manrique][@marina-manrique] [@epareja][@epareja] +We are focused on bringing more genomics data to Bio4j. We are already working on ways of modeling sequences and position-based (annotations) data in a graph paradigm, which we will use for the integration of Human genome data, including assemblies and annotations integrated with the rest of Bio4j graphs. -- **ETA?** Human genome data, other genomic data. support for stabbing queries etc -- **ETA?** [Reactome](http://www.reactome.org/) +[Reactome][Reactome] is a possibility, as sequence data: RefSeq? others? -## Scala API +- **People** [@eparejatobes][@eparejatobes] [@rtobes][@rtobes] [@marina-manrique][@marina-manrique] [@epareja][@epareja] +- **ETA** end of April for the human genome data? -**People** [@eparejatobes][@eparejatobes] [@laughedelic][@laughedelic] +## Bio4j Scala API -- **ETA?** based on Scarph, the work of the nice guys at [oh no sequences!](http://ohnosequences.com). If you're working (or plan to) work with graphs in Scala, definitely keep an eye on this!! Incredibly expressive super typed. Complete interoperability with the Java API in terms of data -- **ETA?** AWS deployment based on [Statika](http://ohnosequences.com/statika) +Based on _Scarph_, the work of the nice guys at [oh no sequences!](http://ohnosequences.com). If you're working (or plan to) work with graphs in Scala, definitely keep an eye on this!! Incredibly expressive super typed. + +Complete interoperability with the Java API in terms of data; data imported with the Java API will be accessible through the Scala API. We will work first on writing the model schema in Scarph, with AWS deployment based on [Statika](http://ohnosequences.com/statika) coming after that. We will maintain the two (Java and Scala) Bio4j schema representations in sync, making sure that you have access to the same graphs and data. + +- **People** [@eparejatobes][@eparejatobes] [@laughedelic][@laughedelic] +- **ETA** May/June? ## Release and data distribution improvements -**People** [@laughedelic][@laughedelic] [@eparejatobes][@eparejatobes] [@pablopareja][@pablopareja] +We want our data distribution and releases to be more predictable, coherent and automated. There will be in-sync automated data import and releases for the Titan-based data distribution, every **6 months**. You will be able to specify statically which version of the imported data you want to use; for this we will develop a concept of data distribution, which will also depend on the import code that was ran to generate it. The import code will be separated from the Bio4j schema. -- **ETA?** in-sync automated data import and releases, every 6 months. Predictable, stable, coherent, automated. -- **ETA?** small testing data subset based on SwissProt. +On a different angle, we are going to start offering a smaller data subset based on SwissProt, mainly for testing or exploratory purposes. We hope that this will lower the entry barrier for those who just want to play with Bio4j and see what it has to offer. - +- **People** [@laughedelic][@laughedelic] [@eparejatobes][@eparejatobes] [@pablopareja][@pablopareja] +- **ETA** September? ## Java API improvements -**People** [@eparejatobes][@eparejatobes] [@laughedelic][@laughedelic] +The work here will mostly be on taking Angulillos to 1.0 and and start the development of the 1.x series, which will have support for an even more expressive API. -- **ETA?** extend angulillos with more sophisticated combinators for traversals -- **ETA?** use any Tinkerpop3 backend! use Bio4j with virtually _any_ graph db +For the 1.x series, we want to extend angulillos with more sophisticated combinators for traversals. Use any Tinkerpop3 backend! use Bio4j with virtually _any_ graph db. TinkerPop is now [Apache TinkerPop](https://tinkerpop.incubator.apache.org/). -## Neo4j distribution +- **People** [@eparejatobes][@eparejatobes] [@laughedelic][@laughedelic] +- **ETA** April for Angulillos 1.0, October? (depends on TinkerPop3) for Angulillos 1.x first releases -**People** [@pablopareja][@pablopareja] [@eparejatobes][@eparejatobes] +## Neo4j distribution -- **ETA?** Finish the implementation of angulillos-neo4j -- **ETA?** write bio4j/bio4j-neo4j +We could finish the implementation of angulillos-neo4j, write bio4j/bio4j-neo4j. Is this actually valuable? If we develop a version of angulillos capable of wrapping any Tinkerpop3-compatible graph DB, we could use the tinkerpop3 version of Neo4j with that. -Is this actually valuable? If we develop a version of angulillos capable of wrapping any Tinkerpop3-compatible graph DB, we could use the tinkerpop3 version of Neo4j with that. +- **People** [@pablopareja][@pablopareja] [@eparejatobes][@eparejatobes] +- **ETA** October/November? ## Documentation -[@eparejatobes][@eparejatobes] [@rtobes][@rtobes] [@pablopareja][@pablopareja] [@marina-manrique][@marina-manrique] +Examples for every graph, model docs integrated with the source code. A paper; by the time this post gets public we should already have a preprint. -- **ETA?** examples for every graph, model docs integrated with the source code -- **ETA?** a paper; by the time this gets public we should already have a preprint - -## Datavis +- **People** [@eparejatobes][@eparejatobes] [@rtobes][@rtobes] [@pablopareja][@pablopareja] [@marina-manrique][@marina-manrique] +- **ETA** April/May? -**People** [@pablopareja][@pablopareja] [@rtobes][@rtobes] [@epareja][@epareja] - -In principle they would all be data visualizations that don't imply server requests. _(That doesn't mean that we won't be developing webapps in the future but we can first get a lot from what we already have without complicating things much more)_ We could include: - -- A few _dashboards_ built with [dc.js](http://dc-js.github.io/dc.js/) This kind of dataviz is quite nice to play with and people generally just love it _(even though they might not understand what's going on too much and they just click randomly at the charts to see what happens... :) )_ -- We should definitely have some sort of minimally interactive visualization of Bio4j data model, IMHO this is crucial not only for people that are willing to use Bio4j but also to get the big picture of what kind of data is included in the database. -- A set of biologically-wise interesting/useful visualizations _( @rtobes @marina-manrique @epareja @eparejatobes please some help here! ;) )_ + [@eparejatobes]: https://github.com/eparejatobes [@pablopareja]: https://github.com/pablopareja @@ -85,4 +81,8 @@ In principle they would all be data visualizations that don't imply server reque [@rtobes]: https://github.com/rtobes [@marina-manrique]: https://github.com/marina-manrique [@epareja]: https://github.com/epareja + +[TinkerPop]: https://tinkerpop.incubator.apache.org/ +[Reactome]: http://www.reactome.org/ + From 22a40a03be2795b0bbc6646c93ab854d723c9a7f Mon Sep 17 00:00:00 2001 From: Eduardo Pareja-Tobes Date: Wed, 18 Mar 2015 17:26:26 +0100 Subject: [PATCH 08/10] minor formatting edits --- source/_posts/2015-03-16-bio4j-a-roadmap.markdown | 2 -- 1 file changed, 2 deletions(-) diff --git a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown index b1a296a..3cb7d00 100644 --- a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown +++ b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown @@ -14,8 +14,6 @@ tag: - overview --- -# Bio4j: a roadmap - > The scope for this is: what's going to happen during 2015 in Bio4j. Right now this is just a list of points I want covered. Feel free to add / remove things, or comment in the commits if you prefer. > > **ETA**: Estimated time of arrival From cd98d9b07f00bdad8d8c729a0137cc7a507f5765 Mon Sep 17 00:00:00 2001 From: Eduardo Pareja-Tobes Date: Wed, 18 Mar 2015 17:33:04 +0100 Subject: [PATCH 09/10] mention Bio4j 1.0 --- source/_posts/2015-03-16-bio4j-a-roadmap.markdown | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown index 3cb7d00..ef0b844 100644 --- a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown +++ b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown @@ -14,7 +14,9 @@ tag: - overview --- -> The scope for this is: what's going to happen during 2015 in Bio4j. Right now this is just a list of points I want covered. Feel free to add / remove things, or comment in the commits if you prefer. +> The scope for this is: what's going to happen during 2015 in Bio4j. The goal I see for this year is **Bio4j `1.0`**; what's so special about `1.0`? From wikipedia: _a major milestone, indicating that the software is "complete", that it has all major features, and is considered reliable enough for general release_. +> +> Right now this is just a list of points I want covered. Feel free to add / remove things, or comment in the commits if you prefer. > > **ETA**: Estimated time of arrival > @@ -70,6 +72,10 @@ Examples for every graph, model docs integrated with the source code. A paper; b - **People** [@eparejatobes][@eparejatobes] [@rtobes][@rtobes] [@pablopareja][@pablopareja] [@marina-manrique][@marina-manrique] - **ETA** April/May? +## Bio4j 1.0 + +The idea is that by the end of 2015 we should have a API-stable, tested, super-cool version of Bio4j which will be Bio4j 1.0. + From 198e8e4d4ffb3bd8ecb996ffabbcee2a30257d64 Mon Sep 17 00:00:00 2001 From: Eduardo Pareja-Tobes Date: Wed, 18 Mar 2015 17:38:27 +0100 Subject: [PATCH 10/10] add requisites for Bio4j 1.0 --- source/_posts/2015-03-16-bio4j-a-roadmap.markdown | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown index ef0b844..6a435c6 100644 --- a/source/_posts/2015-03-16-bio4j-a-roadmap.markdown +++ b/source/_posts/2015-03-16-bio4j-a-roadmap.markdown @@ -74,7 +74,13 @@ Examples for every graph, model docs integrated with the source code. A paper; b ## Bio4j 1.0 -The idea is that by the end of 2015 we should have a API-stable, tested, super-cool version of Bio4j which will be Bio4j 1.0. +The idea is that by the end of 2015 we should have a API-stable, tested, super-cool version of Bio4j which will be Bio4j 1.0. We see as must-have for that + +1. a stable API and model, available in both Java and Scala versions +2. comprehensive documentation and examples +3. solid, easy to use tools for AWS deployment +4. integrated data covering all the structured data needed for the most common Bioinformatics tasks +5. automated periodic data releases