# SBML parser

**URL:** <https://discourse.julialang.org/t/sbml-parser/54915>\
**Category:** Biology, Health, and Medicine\
**Tags:** question, sbml\
**Created:** [February 9, 2021, 10:28am UTC](https://discourse.julialang.org/t/sbml-parser/54915 "2021-02-09T10:28:08Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![Elmo](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/elmo/32/17979_2.png) [@Elmo](https://discourse.julialang.org/u/Elmo)\
**Post date:** [February 9, 2021, 10:28am UTC](https://discourse.julialang.org/t/sbml-parser/54915/1 "2021-02-09T10:28:08Z")

</div>

Is anyone actively working on an SBML parser? I saw [this](https://discourse.julialang.org/t/a-list-of-small-self-contained-julia-projects/8209/2) and [this](https://discourse.julialang.org/t/developing-annotation-standards-for-sciml-to-support-reproduceability-of-published-work/47992/2) but can’t find any status updates. I am busy building a Julia version of Cobrapy (much more expansive than [COBRA.jl](https://github.com/opencobra/COBRA.jl), which seems to be restricted to distributed FBA type problems) that needs to be able to read SBML models.

I have no problem developing a parser from scratch e.g. by providing bindings to SBML’s C api (or Python’s api, not sure which is the better route?) but I don’t want to duplicate work if there is already a parser being developed…

Any suggestions etc. are welcome!

---

<div class="post-metadata">

**Author:** ![ChrisRackauckas](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/chrisrackauckas/32/77_2.png) [@ChrisRackauckas](https://discourse.julialang.org/u/ChrisRackauckas)\
**Post date:** [February 9, 2021, 12:22pm UTC](https://discourse.julialang.org/t/sbml-parser/54915/2 "2021-02-09T12:22:36Z")

</div>

Someone just put a binarybuilder thing in about one IIRC? I’d have to dig around.

---

<div class="post-metadata">

**Author:** ![giordano](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/giordano/32/2166_2.png) [@giordano](https://discourse.julialang.org/u/giordano)\
**Post date:** [February 9, 2021, 1:22pm UTC](https://discourse.julialang.org/t/sbml-parser/54915/3 "2021-02-09T13:22:40Z")

</div>

[https://github.com/JuliaPackaging/Yggdrasil/pull/2458](https://github.com/JuliaPackaging/Yggdrasil/pull/2458)

This seems to be the repository where it is used: [GitHub - LCSB-BioCore/SBML.jl: Julia interface to the Systems Biology Markup Language (SBML) library](https://github.com/LCSB-BioCore/SBML.jl). CC: @laurentheirendt

---

<div class="post-metadata">

**Author:** ![Elmo](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/elmo/32/17979_2.png) [@Elmo](https://discourse.julialang.org/u/Elmo)\
**Post date:** [February 9, 2021, 1:28pm UTC](https://discourse.julialang.org/t/sbml-parser/54915/4 "2021-02-09T13:28:51Z")

</div>

Excellent, this is exactly what I was looking for! Thanks!

---

<div class="post-metadata">

**Author:** ![Elmo](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/elmo/32/17979_2.png) [@Elmo](https://discourse.julialang.org/u/Elmo)\
**Post date:** [June 16, 2021, 7:04am UTC](https://discourse.julialang.org/t/sbml-parser/54915/5 "2021-06-16T07:04:21Z")

</div>

In case anyone has a similar question, lots of things have changed since I asked this question. In addition to the [SBML.jl](https://github.com/LCSB-BioCore/SBML.jl) parser package linked to above, Julia also now has a very high quality constraint based reconstruction and analysis package, called [COBREXA](https://github.com/LCSB-BioCore/COBREXA.jl), as well as a Julia interface to `equilibrator_api`, called [eQuilibrator.jl](https://github.com/stelmo/eQuilibrator.jl), in case you want to combined thermodynamics with cobra methods.