1. Mass fingerprint software:
Input: a peak list, a protein database in fasta format
Output: the protein(s) that are most likely to generate the mass spec.

2. Non-coding gene prediction: (Taken by Russel Dickson)
Input: a genome
Output: all the possible non-coding gene.

3. Mass spec data peak picking
Input: A mass spec
Output: the centroided, deisotoped, charge-deconvoluted spectrum.

4. Retention time prediction software
Input: A few control peptides with known RT. A list of peptides with unknown RT.
Output: RT for the unknown peptides
Requirement: calculate your own RT coefficients by finding some training data on the internet.

5. Genome assembler
Input: Many reads
Output: the contigs and super-contigs.

6. Multiplex PCR primer designer
Input: Many PCR regions and length requirements
Output: PCR primers with the closest melting temperature.