About me
I currently work for the University of Newcastle upon Tyne as a Junior Research Associate/Bioinformatician. The main area of my research is focused on the mitochondrial disease Leber’s Hereditary Optic Neuropathy (LHON) and the application of bioinformatics to highlight disease gene candidates via the retrieval, integration and knowledge mining of distributed data.
After graduating in Applied Biology from Northumbria University I decided to stay in Newcastle. After more than a year of job hunting whilst slaving away in some soul destroying call centres I finally landed a job for a biotech company in the North East. I was employed as an Analyst mainly performing endless HPLC with the odd bit of PCR and sequencing in the genetics lab. It wasn’t long before I realised lab work was not something I could see myself doing for the rest of my career. It just didn’t appeal to me anymore. However, I was still fascinated by biology, mainly genetics and still wanted to pursue this field in some form.
After checking career supplements in New Scientist and Nature for new jobs and courses, a bioinformatics masters seemed like the perfect answer. So far so good. I really enjoyed the course and learnt a vast amount in a short space of time. Don’t get me wrong this was no holiday, some problems had me baffled for days even weeks resulting in me setting up camp in the computing room because it felt like there weren’t enough hours in the day. It was certainly worth it in the end.
On a lighter note Newcastle is a great place to live. The quayside is undergoing some major developments and the nightlife is getting better all the time. It has everything to offer depending on your interests. The Bigg Market is a popular choice for a cheap and boozy night on the town but my favourite places are in and around the Central Station area
3 comments so far
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Hey,
I’ve seen that you have a lot of experience with Taverna. I just started using it and although it looks intuitive in theory, I have been having problems using it. As a first task, all I wanted to do was to load a file with multiple sequences and trim their signal peptide. I thought about using cutseq (from EMBOSS) but my pipeline was spitting the wrong results. Can you give me a hint on how to get it done?
Hi,
I have just tried cutseq in Taverna and it seems to be working. Could
you send me your workflow XML file?
What inputs are you specifying and what results are you getting from
this service?
Thanks
Kieren
Hi Kieren,
I am new to taverna.I developed an api fetches results from a database.These results are returned to the users in structure/sequence objects based upon the function invoked.I want to integrate this api to taverna.
Generally my api can be used bya different program where in the user has to create an api object say obj.When the object is created the JDBC connection is set up.Then he/she can invoke obj.getXYZ(…) functions.These fucntions execute a query on the database get the results in the form of biojava objects.
How can I do all this in taverna?I tried using API-consumer but some where I am going wrong as I am getting an empty list.