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The Seven Deadly Sins of Bioinformatics Professor Carole Goble The University of Manchester, UK The myGrid project

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1 The Seven Deadly Sins of Bioinformatics Professor Carole Goble The University of Manchester, UK The myGrid project myExperiment OMII-UK

2 We’ve been developing software and ontologies and data and stuff with and for Bioinformatics and Bioinformaticians for a long time. “though it took two years before we understood each other!” Andy Brass, Professor of Bioinformatics

3 3

4 my Grid Taverna Workflow Workbench

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6 The Seven Deadly Sins of Bioinformatics BOSC 2007 8091views (02-June-2008) From an original idea by Stevens and Lord

7 7 Methodology Email a handful of bioinformaticans. Stand well back. Collect. Edit. Therapy on the cheap. We all felt better.

8 8 I am grateful to… Phil Lord (University of Newcastle) Anil Wipat (University of Newcastle) Matthew Pocock (University of Newcastle) Robert Stevens (University of Manchester) Paul Fisher (University of Manchester) Duncan Hull (Manchester Centre for Systems Biology) Norman Paton (University of Manchester) Marco Roos (University of Amsterdam) Rodrigo Lopez (EBI) Tom Oinn (EBI) Andy Law (Roslin Institute) Graham Cameron (EBI)

9 They came up with more than seven. But I beat them into submission. Many are highly inter-related. Hopefully they are all too familiar.

10 10 The Traditional Sins…. 1.Lust 2.Gluttony 3.Greed 4.Sloth 5.Wrath 6.Envy 7.Pride

11 11 The Sins of Bioinformatics 1.Parochialism and Insularity 2.Exceptionalism 3.Autonomy or death! 4.Vanity: Pride and Narcissism 5.Monolith Meglomania 6.Scientific method Sloth 7.Instant Gratification

12 12 Parochialism “being provincial, being narrow in scope, or considering only small sections of an issue.” Insularity “a person, group of people, or a community that is only concerned with their limited way of life and not at all interested in new ideas or other cultures.” Sin 1: Parochialism and Insularity

13 13 Reinvention of the Wheel Rediscovering the same old problems, techniques, methods. Creating…Yet another … –identity scheme. –representation mechanism for data. –ontology. –data warehouse. –integration framework. –query or ontology or workflow language. Result? Misery. But more work for the boys….

14 14 Q92983 O00275 O00276 O00277 O00278 O00279 O00280 O14865 O14866 P78507 WSL-1 protein Apoptosis-mediating receptor DR3 Apoptosis-mediating receptor TRAMP Death domain receptor 3 WSL protein Apoptosis-inducing receptor AIR Apo-3 Lymphocyte-associated receptor of death LARD GENE: Name=TNFRSF25 Q93038 = Tumor necrosis factor receptor superfamily member 25 precursor P78515 Q93036 Q93037 Q99722 Q99830 Q99831 Q9BY86 Q9UME0 Q9UME1 Q9UME5 Annotation history:

15 15 Andy Law's Third Law “The number of unique identifiers assigned to an individual is never less than the number of Institutions involved in the study”... and is frequently many, many more.

16 Bioinformatics is about mapping one schema to another, one format to another, one id scheme to another. Comparative Genomics? Comparative Bioinformatics! What a waste of time. But a handy distraction from doing some Real Science™.

17 17 Andy Law’s First (Format) Law “The first step in developing a new genetic analysis algorithm is to decide how to make the input data file format different from all pre- existing analysis data file formats.” crimap femalemale Keightly Knott and Haley 01 10 12 When they use ‘3’ and ‘4’ we will know they are doing it deliberately.

18 18 Organism databases 250+ metabolic pathway databases. Generic Model Organism Database Toolkit. FlyBase, WormBase, SGD, BeeBase and many other large and small community databases Yet another database … Yet another Integration Platform… Warehouses, Views, Mashups, Workflows … Goble and Roberts, The state of the nation in data integration in the Life Sciences. JBI.

19 19 BioBabel bioperl biojava biopython bioruby biophp biosql biouml bioeclipse biofoo biobar bio*

20 20 Computer Science? No thanks! Ontology and Knowledge Representation Languages Database Schemas Workflow systems Integration platforms Programming Languages Tools

21 21 Why don’t biologists modularise OWL* ontologies properly? Er, well, like how should we do it “properly” and where are the tools to help us? We don’t know and we haven’t got any. But here are some vague guidelines. W3C Semantic Web for Life Sciences mailing list, 2005 *The W3C Web Ontology Language

22 A few months in the laboratory can save a few hours in the library. Westheimer's Law A few years at the computer can save a few hours on Google.

23 23 Reuse Rocks. Collaboration through workflow and web services VL-e Project “instant collaboration” with Martijn Schuemie (Rotterdam) through a web service that discloses their protein synonym data. Exchanging services and (sub)workflows with food scientists. Web services make that easier. This isn’t the workflow – its just a picture of one!

24 24 Of Mice and Cows A Trypanosomiasis in Cattle workflow (by Paul*) reused without change for Trichuris muris Infection (by Jo). Identified the biological pathways believed to be involved in the ability of mice to expel the parasite. Workflows are memes. Scientific commodities. To be exchanged and traded and vetted and mashed. Users add value. *Fisher P et al A systematic strategy for large-scale analysis of genotype–phenotype correlations: identification of candidate genes involved in African trypanosomiasis, Nucleic Acids Research, 2007, 1–9

25 25 Sin 2: Exceptionalism Biologist exceptionalism Biological exceptionalism Biology exceptionalism A root cause of Reinvention Syndrome “Bioinformatics is special” “Our domain specific outcomes requires- specific approaches and technologies”

26 26 Biologist exceptionalism I know there is already a gene name for that gene, but, I don't like it and it doesn't fit in with my schema. It would be better if I wrote the script I need so I know what it does, how it does it and how to modify it later because I haven’t specified what it was supposed to do in the first place. I’m different. We are all individuals.

27 27 I am considerably more complex than you… “There are proteins, and there are records about proteins. Records come in different formats. If I make a statement using this url, is it about the record? or the protein?” Alan Ruttenberg “[Usually] we have one entry per gene. We have several entries for a single gene when description of variations are too complicated to describe in FT lines (of course, this criteria depends on the annotator). For viruses, it is much more messy, due to ribosomal frame-shifts. Formalise that!” Eric Jain UniProtDB er…decomposition and untangling?

28 28 Biology Exceptionalism Drawing graphs of data sets over time. Stop it. The real problem is complexity not scale. The number of data sets, their diversity and how they overlap. How they change. Their reliability.

29 29 Biological exceptionalism “Biology is all exception.” Don’t complicate everyone’s life for the sake of a few esoteric cases. –Cameron’s 5 th Commandment of Curation Exceptionalism paralysis. Gather requirements expansively, prune ruthlessly The EMBL/GenBank/DDBJ/Feature Table

30 30 With added churn, indifference to users and monopoly mentality. Sin 3: Autonomy or death! Compounded by the Early Adopter tendency of the community “Hell is other people’s systems” as Jean Paul Sartre would have said if he had been a bioinformatician.

31 31 Autonomy IS death! I’ll Change my interface / format whenever I feel like it, despite the fact I wanted lots of users and I have lots of users who depend on this. And I won’t bother to debug either or provide backwards compatibility. So there. –BioMART changed 4 times in the 2007. –NCBI changes as it fancies. –Ensembl relational schema. –Early BioJava. Churning for change sake Professional

32 32 No tool is an island… Assume –only we will use it, whatever it may be. –that it will be freestanding and unlinked to anything else. –that it will always work and will keep on working. –That everyone will understand it. “Well I know what I mean. And so does my friend. So I don’t need to specify it. Or document it properly. Or keep the metadata up to date.” Never mind the interface, just look at my implementation! Metadata, Models, Interfaces, Services matter.

33 33 Workflow commodities Workflow published with its paper and its data set. So what happens when I want to run this workflow again? Is the service dead? Is the dataset still there? Was it designed to be reproduced or reused in the first place?

34 34 The myGrid Service DeCrypting Sweatshop notice how tired they look Franck Tanoh Katy Wolstencroft

35 35 Lincoln Stein said a while ago… “An interface is a contract between data provider and data consumer” Document interface; warn if it is unstable Do not make changes lightly –Even little fiddly changes break things –Provide plenty of advance warning When possible, maintain legacy interfaces until clients can port their scripts Support as many interfaces as you can HTML, Text only (better), HTTP, REST, SOAP Easy Interfaces + Power User Interfaces …and he could say it again today.

36 Stability is more important than Standards, Smartness, or the latest Thing that everybody is talking about.

37 37 Sin 4 Vanity Pride Narcissism conceit, egotism or simple selfishness. Applied to a social group, denotes elitism or an indifference to the plight of others

38 38 I know it all. Claiming to know everything about biology and everything about computers. Really irritating to biologists AND computer scientists. Even they don’t claim to know everything about biology or computer science. Computer scientists do know a lot of stuff. And they publish too. “Biologists are the experts on everything because we produce the data” And what would you suggest, Mr. Smartie Pants?

39 39 Think like me! Be like me! Designing good experiments is hard. Workflows are computational experimental protocols. Ergo…. Writing workflows is hard. Writing good workflows is really hard. Writing good reusable workflows is really really hard. Misunderstanding and disrespecting users Building interfaces that only you can use. Not actually using your tools in the field. I understand workflows Workflows are for biologists. My granny can do workflows...

40 A good User Experience outweighs smart features and cool computing. Bummer. Can I use it? Is the user interface familiar? Does it fit with my needs?

41 41 Sin 5: Monolith Meglomania delusions of grandeur. obsession with grandiosity and extravagance. Data mining –“ my data is mine, and your data is mine”

42 42 Integration – the more the merrier. No. –Every link is a potential dead link. –Every dependency finds its way on to your critical path. “Uber-tools” and “Uber-databases” –Ensembl, BioMART etc etc….cost Apps/libraries in bioinformatics workbenches –with loads of crap bundled in, none of it kept up to date, none of it properly integrated. Put it all in a warehouse. –Lots of warehouses and lots of toolkits…GMOD, BioWarehouse, BioMART blah blah…. –50% warehouses fail. (Standish Group)

43 43 The trouble with warehouses Warehouses work? Piffle. They never manage to maintain synchrony with the source data. Mostly they fall down of their own weight!” Graham Cameron, EMBL-EBI "Our ability to capture and store data far outpaces our ability to process and exploit it. This growing challenge has produced a phenomenon we call the data tombs, or data stores that are effectively write-only; data is deposited to merely rest in peace, since in all likelihood it will never be accessed again. Data tombs also represent missed opportunities." Usamma Fayyad Yahoo! Research! Laboratories! We believe that attempts to solve the issues of scientific data management by building large, centralised, archival repositories are both dangerous and unworkable” Microsoft 2020 Science report.

44 44 Distributed Annotation System Reference Server AC003027 AC005122 M10154 Annotation Server AC003027 M10154 WI1029AFM820AFM1126WI443 AC005122 Annotation Server Now we call this a mash up

45 45 Sin 6: Scientific Method Sloth Its easier to think of a new name than use someone else’s. I want my own view over data and views are difficult, so I’ll create my own database. Leads to Reinvention, Exceptionalism Often the result of Instant Gratification

46 46 Ennui Garbage in, garbage out –Running analysis over the wrong datasets –E.g. Identifying chicken proteins in mouse cells. Configuration traditionalism –Not changing the parameters of BLAST. Ever. Top list ennui –If there is a list only looking at the first one. –Look no further than the first Blast hit / first Google hit. Arbitrary cut-offs on rank-ordered result list –Absolute truth above, absolute falsehood below –E.g. differentially expressed genes in microarray analyses.

47 47 Quality Delusions The bioinformatics does not have to be sound, because we only trust wet-lab results anyway. Worrying about errors in experimental data but believing that derived data is always true. Believing Trembl is always right. Believing computational gene predictions are always correct.

48 48 Irreproducible Black Box Science Can you reproduce bioinformatics analyses? –Not collecting the provenance of the analysis. –Not testing during software development. UniGene –What is happening during UniGene clustering? –‘Human’ descriptions (via NCBI), are not exact. –The Human Transcriptome Map project and other microarray analysts ended up reclustering UniGene [Marco Roos]. Stuff In Stuff Out

49 “No experiment is reproducible.” Wyszowski's Law “An experiment is reproducible until another laboratory tries to repeat it.” Alexander Kohn

50 50 Sin 7: Instant Gratification Greed? Gluttony? Always the immediate return. Never investing for the future. The quick and dirty fix. Refusing to model or abstract. Refusing to plan for recording and exchanging. Just getting the next quick fix. The pressure to deliver now and pay later

51 51 Hackery Deliver now, pay later –Producing crap, non-reusable, software because only the biological results matter for publication X. –Collect! Analyse! Er…now what? –NO up to date or useful DOCUMENTATION! Spaghetti-ism –Over-indulgence in PERL –Over-indulgence in Ascii Art flat files. –Modelling a system by hacking up XSD fragments on a whiteboard. –Writing perl scripts that resemble my high-school BASIC of the 80s.

52 52 Law's Second Law “Error messages should never be provided” corollary... “If error messages are provided, they should be utterly cryptic so as to convey as little information as possible to the end user”

53 53 Blind faith in XML (or any mechanism) “It’s in XML, thus all data integration problems are solved.” “The good thing about XML is that it is human readable”. !!*£!*! XML

54 54 Blind Faith in Foo. There's a new thing to use. we don't understand it yet. so it sucks up all the stuff we already know we don't understand. Lack of appreciation about exactly what the new technology addresses in itself before trying to make it work for us.

55 55 Pioneering development methods Development by anecdote –I heard in the pub that the way to go was Foo. –Though I have no idea what Foo is or why it is the way to go. Design by hacking –It would be better if I wrote the script I need so I know what it does, how it does it and how to modify it later because I haven’t specified what it was supposed to do in the first place. –Hmmm…..We call that Extreme Programming or Emergent Semantics or Web 2.0 in CS.

56 56 At the other end of the spectrum… Often found in industry Over-engineered solutions Delivered too late That solve a problem the users didn’t know they had Or are hard to use Or wire their favourite tool in

57 57 Sin Summary Maybe only one “original sin” in bioinformatics. Parochialism and Insularity Autonomy or death! Vanity: Pride and Narcissism Monolith Meglomania Scientific method Sloth Instant Gratification Reinvention Churn Exceptionalism

58 Why do these sins exist? Can we become less sinful? Are bioinformaticians particularly naughty? No naughtier than Computer Scientists. And its all very hard. Though they are naughty…

59 59 Forgive us our sins…. 1. Reward Culture The Selfish Scientist and Self-promotion, Research vs Production, Reuse is Hard 2. Mechanism evangelism More than one mechanism New and my shiny Gadget syndrome 3. Gang warfare If you are not with us you are against us Interdisciplinary mistrust and conflict 4. Blazing the trail Invention, not Reinvention Delivery bulge 5. Fear and Trust Luddism Trust (or lack of it) 6. Its Hard Hybrid Exhaustion The Selfish Scientist and Self-promotion Research vs Production Reuse is Hard More than one mechanism New and my shiny Gadget syndrome If you are not with us you are against us Interdisciplinary mistrust and conflict Invention, not Reinvention Delivery bulge Luddism Trust (or lack of it) Hybrid Exhaustion Long Jump

60 60 The Selfish, Self-interested Scientist Reputation. Results right now. Win. More funds! Fear of dependency. Fear of being left behind. Understand the incentives and barriers to adoption. “A biologist would rather share their toothbrush than their (gene) names” Mike Ashburner, Professor Genetics, University of Cambridge, UK

61 61 Funding and Social structures Are against shareable reusable software/ontology/database/thing 1.Self-promotion –I can publish every new monolithic thing and I can’t publish if I reuse someone else’s thing. 2.Novelty vs Standards –Standards are boring “blue collar” science (Quackenbush) 3.Research vs Production Confusion –How do you get funding for production software other than claiming to be researching stuff? –How do you get a publication out of a bit of research software without claiming a potential user-base? –I don’t want to be a long-term service provider! Short Jump

62 62 I may have the solution, fund my next project I may have the solution, fund my next project I may have the solution, fund my next project I may have the solution, fund my next project I may have the solution, fund my next project I may have the solution, fund my next project I may have the solution, fund my next project I may have the solution, fund my next project I may have the solution, fund my next project I may have the solution, fund my next project I may have the solution, fund my next project [Marco Roos]

63 63 Reuse is Hard Writing reusable workflows is hard. –Local services. Permissions. Licences. Writing reusable services is hard. –Predicting the unknown required by the unknown. –Its an effort –What is in it for me? Helping out my competitors! Forcing me to support others? Finding and using “reusable” workflows and services and tools is hard –Where do you go?? What does it DO??

64 64 My New Gadget Syndrome This is inherited from Computer Science I fear. Sorry. A few evangelistic voices, very loud, vested interest, for their application, win.

65 65 More than One Mechanism Muddle Global Identity naming mechanism for data objects in the Life Sciences. LSIDs and URIs and PURLs. WS-Naming and all its friends.{db}:{id}{db}/{id}{db W3C Semantic Web Health Care and Life Sciences Interest Group

66 66 Use My Mechanism If you are not with us you are against us “Why do this? It's already been solved by Foo - the massively unwieldy, slow-moving, monolithic, meeting paralysed international effort for Things Mentioning the word Foo”. If a group is working in a field, you get bullied for trying out something different. You may doing something different, but you use some common words.

67 67 Pragmatists Aesthetics Philosophers Life Scientists Capulets Knowledge Representation Montagues A means to an end Content providers Theoreticians The end Mechanism providers Endurants, Perdurants, Being, Substance, Event Spiritual guides The Montagues and The Capulets …SOFG 2004, KCap 2005, Comparative and Functional Genomics 2004 Oh No it’s the OBO War

68 Endurants, Perdurants, Being, Substance, Event Discipline gang warfare The Montagues and The Capulets, Comparative and Functional Genomics, 2004 The Ontology War Short Jump

69 69 Invention, not Reinvention BioMOBY pre-dates (Semantic) Web service revolution –Though not 20 years of SOA OBO and OBO-Edit pre-dates OWL and Protégé-OWL –Though not 20 years of Knowledge Representation. Taverna pre-dates a reliable Open Source BPEL engine –Though not 20 years of lambda and pi calculus and petri nets. There ARE features that Bioinformatics needs that other solutions don’t cater for. And solutions needed URGENTLY

70 70 Delivery Bulge

71 71 Luddism Refusing to have biology go beyond a cottage industry. Being scared to do it properly. Railing against big science The cult of amateurism. [Stevens]

72 Trust I don’t trust your code I don’t trust your data I don’t trust you will still be around in one year I don’t trust your workflow I don’t trust you will use my data / workflow / code properly

73 73 Hybrid exhaustion and pressure. Biology + Computing + Bioinformatics It. Is Hard.

74 What can we do to be less sinful? Make sharing easier Make sharing rewarded Think Components Only standardise the minimum Embed bioinformaticians and computer scientists Presume naughtiness

75 75 Think Safe Sharing of Stuff Understanding outside my expertise. e.g. sources of error. A comprehensive catalogue of web services A Facebook for workflow builders. Learn from others. Even Computer Science. And other Sciences. Try and create a culture of raising quality. Somehow.

76 76

77 77 Think Components Stop building monolithic solutions Component-ise Bioinformatics –Loosely coupled systems –Stable APIs, standardised metadata. –Design to combine. –Sort out the naming/id problem –If you can’t agree, agree on the bridge. –Virtualise Raise the level of abstraction –Less Perl, more workflows –Enable users to extract the data they need without hassling you. “Standardise messages not structures” Graham Cameron Web Services

78 78 Think how it Really Is™… …incremental change …others use our stuff …others add value to our stuff …scientific naughtiness deal with it, or expose it. end to black boxes workflows as a route to transparency open notebook science scary stuff. Short Jump

79 79 Embrace Naughtiness Presume scientific practice naughtiness –Try to deal with it, or expose it. –Transparency and accurate collection and reporting. –Provenance. –A prerequisite to publication. –The end of Black Box Science. –Peer pressure. E.g. Workflows, but will a scientist give away their secrets or expose their mistakes?

80 80 Think User and Developer together Embed Bioinformaticians with Computer Scientists and Biologists

81 81 Think Web 2.0 Design Patterns De Roure, D. and Goble, C. (2008) Six Principles of Software Design to Empower Scientists. IEEE Software (to appear). 1.The Long Tail 2.Data is the Next Intel Inside 3.Users Add Value 4.Network Effects by Default 5.Some Rights Reserved 6.The Perpetual Beta 7.Cooperate, Don't Control 8.Software Above the Level of a Single Device

82 “Other men's sins are before our eyes; our own are behind our backs” Seneca Roman philosopher, mid-1st century AD

83 “Should we all confess our sins to one another we would all laugh at one another for our lack of originality” Kahlil Gibran Lebanese born American philosophical Essayist, Novelist and Poet. 1883-1931

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