The AP11 project (Proteomic-genomic Nexus) has reached end of development and we are happy to announce the proteomic-genomic nexus tools are available for the general public.

User Testing has been completed on the AP11 application. Our user testing was completed by Ignatius Pang and Aidan Tay, who have extensive experience in genomics and proteomics and are part of the Ramaciotti Centre at UNSW. They used realistic data (in terms of content and size) for the testing, and their feedback was invaluable in helping produce a high quality solution. Read on for more info about their findings.

Marc Wilkins presented a poster titled “Validation of Genomes and Transcriptomes with Proteomics Data” at the 18th meeting of the Australian Proteomics Society at Lorne. Marc reported that the poster was of exceptional interest. He said that over the two hour session, there was a constant stream of people keen for an explanation. Groups were from local facilities (including APAF) along with some from overseas.

This is a great success for the project and we look forward to hearing more as people start trying out the software.

link to the poster

Demo number two was about seeing the samifier and the predicted proteins implemented in Java. We had a chat too about how the web app was going.

Working with reverse strand proteins requires special attention, as the position arithmetic and logic needs to be worked out with care. As developers, we need to have a documented procedure to be able to check amino acid and nucleotide sequences and this post is an attempt in that direction.

We had our first sprint demo on the 27/Aug, which didn’t go without its hurdles. We showed the web app site, with initial user registration, user management and experiments page.

Ignatious just presented the project to the rest of the lab. One finds the slides here. The general feedback was positive, bringing some ideas of what features we could have for IGV.

On the other hand, development just started on the samifier and the team is getting closer to a first cut. It is a prototype written in Ruby. It won’t have reverse strand handling, but will be able to generate fragments of forward encoded proteins, even if they are split by introns.

The Sofware Requirements Specification (SRS) is live as a set of pages answering some general questions about the project.

Here they are:

1. Who is doing this? Product team
2. Why is it worth doing? Main goals
3. Who is this for? Users
4. What is the added value? Specific goals
5. How is it going to work? Features and architecture
6. What will be the outcomes? Products and outcomes

We will be updating these entries as we go and are a key reference in the evolution of the project.