DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysis.

A central tenet of reproducible research is that scientific results are published along with the underlying data and software code necessary to reproduce and verify the findings. A host of tools and software have been released that facilitate such work-flows and scientific journals have increasingly demanded that code and primary data be made available with publications. There has been little practical advice on implementing reproducible research work-flows for large 'omics' or systems biology data sets used by teams of analysts working in collaboration.

Long-term results of two Swiss AML studies.

The Swiss group for clinical cancer research (SAKK) completed two first line protocols for the treatment of acute myelogenous leukemia (AML). In the first protocol (SAKK AML 74, from August 1974 to April 1977; 107 patients) the effectiveness of immunization with viral oncolysate during maintenance treatment was tested. After successful induction treatment, the patients were randomized in two groups: Group A: monthly maintenance chemotherapy for 2 years and group A+IT, which received the same maintenance chemotherapy regimen plus, on day 15, injection of viral oncolysate.

[Chemo-(hormonal)-therapy of advanced ovarian neoplasms in FIGO stages III and IV. Prospective SAKK-study 20/71].

From 1971 to 1974 89 patients with advanced ovarian cancer (FIGO-stage III-IV), admitted to seven centers of the Swiss Group for Clinical Cancer Research (SAKK), were randomly allocated to three different treatment schedules: cyclophosphamide (CYT) alone or CYT in combination with either medroxyprogesterone acetate (GEST) or 5-fluorouracil (FU). Results in 71 evaluable patients (according to standardized group criterial) were as follows: 1. The overall remission rate was 48% (34 out of 71 patients) with no clear-cut statistical difference between the three treatment schedules but a firm trend towards higher remission rate with CYT + FU (58% as compared to 42% with CYT alone).