Porting and optimising star: a case study of suffering and surfacing

ABSTRACT

This paper has three main parts. The first part is a description of our project STAR. It explains what our program does and what makes it special compared to other similar programs. The second part pertains to the porting of our program to other platforms. It enumerates the errors of our ways, how we struggled to overcome them and what we learned in the process. The last part narrates our strategy to optimise the program. We will explain why we deviated from the general accepted strategy to optimise those parts with the highest potential gain.

REFERENCES

• 1: Abrahams, J.P., Berg, M.v.d., Batenburg, E.v. & Pleij, C. Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Research 18(10)3035-3044 (1990).
• 2: F. H. D. van Batenburg, L-one-two-three (L1:..L2:..L3:) considered harmful, ACM SIGAPL APL Quote Quad, v.21 n.4, p.330-337, Aug. 1991
• 3: M. A. Jackson, Principles of Program Design, Academic Press, Inc., Orlando, FL, 1975
• 4: Kerf, J.L.F. de Second generation APL and ISO APL Extended (APL 9x). APL-CAM J.13(1)189-270 (1991).
• 5: Mavor, J.W. & Manner, H.W. General biology p.565; New York, MacMillan Company (1966).
• 6: Zuker, M. & Stiegler, P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acid Research 9(1) 133-148 (1981).

INDEX TERMS

Primary Classification:
  J. Computer Applications
  J.3 LIFE AND MEDICAL SCIENCES
      Subjects: Biology and genetics

Additional Classification:
  D. Software
  D.3 PROGRAMMING LANGUAGES
      D.3.2 Language Classifications

          Nouns: APL
      D.3.4 Processors
          Subjects: Optimization; Translator writing systems and compiler generators

  H. Information Systems
  H.5 INFORMATION INTERFACES AND PRESENTATION (I.7)
      H.5.2 User Interfaces (D.2.2, H.1.2, I.3.6)
          Subjects: Interaction styles (e.g., commands, menus, forms, direct manipulation)

General Terms:
Algorithms, Languages