The ZBIT Systems Biology Software and Web Service Collection


Andreas Draeger

In systems biology, people want to perform dynamic simulations, steady-state analyses and others. SBML is the format to use for the model, but you also need a data structure for use in the software, and as such they developed jSBML.

People build models from KEGG, textbooks and more. They try to rebuild KEGG diagrams in CellDesigner, which is very time consuming. Is there a better way to do this? And, indeed, there are even difficulties with this manual method, as some reaction participants present when you study the record aren’t visible in the associated diagram (e.g. the addition of ATP), which can cause issues for novices. Therefore they developed KEGGtranslator to convert KEGG pathways to various file formats. Another way to add a data source to your model is through BioPAX2SBML. Additionally, they’ve created ModelPolisher which can augment models with information from the BiGG database, which is available as a command-line tool and as a web service. For dynamic simulation, they have a tool called SBMLSquezer, which generates kinetic equations automatically and also reads information from SABIO-RK.

This system was applied to all networks in KEGG. They use SBMLsimulator to run the simulations. They’ve developed a documentation system called SBML2LaTeX which helps people document their models.

Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!

UKON 2016:Making Sense of Description Logics

These are my notes for Paul Warren’s talk at the UK Ontology Network Meeting on 14 April, 2016.

Source 14 April 2016

What can we learn from the theories of reasoning? To understand the difficulties experienced with DLs, and try to mitigate those difficulties. There have been a lot of psychological studies on how people reason. Historically, there have been two camps, the rule-based and the model-based reasoning. Rule-based (syntactic) is where we reason by constructing logical steps akin to those created formally by a logician in a proof. Model-based is about reasoning via constructing mental models which represent the situation (semantic). These two are complemented by a third method (missed that name).


English: John only has sons (implication: he does have children but no daughters)

Manchester OWL: John has_children only Male (implication: if he has children, they are sons, but he might not have any at all)


Mental models

English: John sons

Manchester OWL: John son(s), John has things which are sons

It seems that people are reasoning syntactically, based on the work he has done. Recommendations are then to use syntax where possible to emphasize semantics. However, beware of false equivalences and teach the duality laws as expressed in Manchester OWL syntax and let tools show alternative equivalent statements.

In a study, only half got it right that the following were not disjoint: “has_child only MALE” and “has_child only (not MALE)”. Replacing only with only or none helped a lot.

People didn’t do very well thinking about functional object properties. But why was this? He designed two pieces of reasoning which were equivalent which required 3 reasoning steps to get to the appropriate conclusion. One piece used functional, and the other used the transitive property. People finished the reasoning faster and more got it correct when using transitivity.

Functionality is inherently difficult. They suggest a new keyword solely, to emphasise that it is the object which is unique and not the subject. This showed a significant improvement in performance.

Theories of reasoning and language provide insight and lead to recommendations for modifications to syntax, tool support and training.

Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!

SysMO-DB and Carole Goble, BBSRC Systems Biology Workshop

BBSRC Systems Biology Grantholder Workshop, University of Nottingham, 16 December 2008.

Systems Biology of Microorganisms. 11 projects from 91 institutes, whose aim is to record and describe the dynamic molecular processes occurring in microorganisms in a comprehensive way. These projects have no one concept of experimentation or modelling, which makes it tough for information exchange. Further, there are issues of people having their own solutions, suspicions (about sharing data, for instance), data issues (many don't have data or don't store it in a standard way) and resource issues (no extra resources). SysMO-DB started in July 2008, and is a 3 year funded effort (3+3 people in 3 teams over 3 sites). Provide a web-based solution to exchange, search, and disseminate data. Need to retrofit data access, model handling and data integration platform. Because of the large number of groups and projects, they are going to aim for low-hanging fruit and early wins: be realistic, not reinvent, sustainable, and encourage standards adoption.

Just like at CISBAN, where we have implemented a web-based data integration, storage, exchange, and dissemination platform in a standards-compliant way (SyMBA), they have three users: experimentalists, bioinformaticians, and modellers. They're lucky, though, in that they have 6 people to develop SysMO-DB, when CISBAN only has 1. 🙂 And, as with CISBAN and many other data integration efforts, much of the work is social: that is, encouraging those three user types to collaborate and understand each other's work. The social solutions include questionnairs, "PALS" (postdocs and phd students), and Audits and sharing of methods, data, models. They discuss things like what people need or don't need from MIAME. (Personal opinion and question: MIAME is intended as a minimal information checklist. What kind of things, then, don't they need? And would it be worth taking this information back to the MIAME people to possibly modify the guidelines if some aspects of it aren't truly minimal? End personal questions.)

Discovery is done via SysMo-SEEK. How to catalog the metadata, and then have mechanisms for accessing the data from locations other than the host site? There is a single search point over "yellow pages" and assets catalogue. They store metadata on results, not the results themselves (again, just like SyMBA, which stores the metadata in a database, and the results in a remote file store). They use myExperiment for both linking the people and the assets. For models, they're using a local installation of JWS online, which is a database of curated models and a model simulator. There is also some links to semantic SBML from the TRANSLUCENT project.

There are two kinds of processes to store. The first is experimental processes, e.g. SOPs and protocols. They use the Nature protocols format, with the addition of high-level classification through tags. (Personal note: What is the underlying format for storing protocols?) The second type of process is Bioinformatics processes, which are stored as workflows. (Question: Why don't you store protocols as workflows? They can be chained in the same way.)  Taverna is used for this work. One bit of work was using libSBML inside taverna for collaborative model development (Peter Li et al). Another automated (definition of automated in this context?) workflow goes from microarray to pathways and published abstracts. Their consortium wants to exchange information from public data sources, SysMO itself, and excel spreadsheets.

(Another personal aside. FuGE (object model for experimental metadata) and ISA-TAB (tabular format, e.g. spreadsheets) are becoming interchangeable – work is going on between FuGE and ISA-TAB people right now – most recent workshop was last week. This is important, as it was mentioned that bioinformaticians have to deal with spreadsheets (which is true enough!). So, you get the best of both worlds with FuGE / ISA-TAB, without having to define yet another schema. A personal question would be: Why build these various metadata schemas and parsers for spreadsheets (e.g. whatever is used for the Assets catalogue and JERM parsing of spreadsheets) rather than use pre-existing models such as FuGE and formats such as ISA-TAB? Using the FuGE object model does not mean that you have to use all aspects of it – you can just take what you need.Perhaps it was due to the maturity of ISA-TAB at the time the project started, though the specification is now in version 1.0. Will SysMO-DB export and import these formats? There was no time for questions at the end of the talk, so I will try to find out during the lunch period. End aside.)

Trying to map to the relevant MIBBI standard. There is a nice feature that reads spreadsheets from specific locations and automatically loads them into the Assets catalogue. (You can still load them directly into that catalogue.) They are performing a 4-site JERM exchange pilot scheme in Spring 2009.

Great talk – thanks 🙂

These are just my notes and are not guaranteed to be correct. Please feel free to let me know about any errors, which are all my fault and not the fault of the speaker. 🙂

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Congratulations to the Newcastle Uni iGEM Team 2008!

Congratulations, Bug Busters! You didn't just get a gold star, you got a gold award!

Though I was not involved, many of my friends were part of the Newcastle University iGEM 2008 team, either as supervisors or students. You can read more on the Newcastle University iGEM entry wiki page. Of the 84
teams competing, only 16 won gold medals, including, from the UK, Edinburgh,
Imperial and Newcastle.

From the overview of the team's wiki page:

"We aimed to develop a diagnostic biosensor for detecting pathogens.
We wanted this to be cheaply and readily available for deployment in
areas where access to medical resources, such as refrigeration and
sophisticated laboratories, is limited or absent. We chose to use Bacillus subtilis
as a method of delivery due to its ability to sporulate. The sensor
bacteria could then be dried down as spores, which are very stable and
extremely resilient to hostile environmental conditions, and rehydrated
when required. The ambient temperature of much of the developing world
is ideal for the growth of
Bacillus spp. without the use of incubation equipment.

Gram-positive bacteria communicate using quorum communication
peptides. Research has shown that these peptides are extremely
strain-specific. We chose to engineer
B. subtilis 168 to detect
four Gram-positive pathogens by their quorum communication peptides.
The different combinations of quorum communication peptides would be
sensed by the engineered bacterium, and this signal converted into a
visual output as fluorescent proteins such as mCherry, GFP, CFP and
Read more.

Well done!

P.S. Looks like kudos to my old alma mater, Rice University, too! Congrats!

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