Ethnography – a combination of community mapping, participant-observation and in-depth interviews – is a flexible yet rigorous and systematic style of qualitative research, with well established conventions for data collection and analysis [ 33, 34].
Data management plan A. Annotated database structure B. List of coding conventions for data C. List of procedures used to process the data D. Merging criteria (database keys) E. System environment: analysis package (with version), system hardware, input data structure, output data structure, long-term storage environment ii.
However, the need to write customized code will inevitably arise in many projects, and then, HTSeq aims to offer advantages over more narrow programming libraries that focus on specific file formats, e.g. PySam and Picard (http://picard.sourceforge.net/) for SAM/BAM files, by integrating parsers for many common file formats and fixing conventions for data interchange between them.
The ArrayExpress function extracts feature intensity summaries from columns of the raw data files based on the common conventions for the data file sources.
One of the main obstacles for easy use of this data with networks is multiple naming conventions for experimental data and network elements and many-to-many mappings when applying BLAST homology to map across species.
Strict naming conventions for trajectory data (raw, averaged, and filtered on space or time) should help circumvent these problems.
These should be as simple as possible and follow the languages' expected conventions for holding data.
In fact, many of these requirements could be met by using JAR files as ActivePapers, adding just a set of conventions for storing data, metadata, and references inside JAR files.
The following example illustrates the convention for interpreting the data: The hit Band7 → 6 indicates that a particular protein had six MS/MS peptide hits in gel fraction 7. Additional columns indicate the number of residues covered in aa residues and percent of total protein that was covered by the procedure.
The following example illustrates the convention for interpreting the data: The hit MS-31-3 -> TPTAELR 111| represents the result of the third peptide (MS-31 3) identified in the tryptic digest from spot number 31 (MS- 31-3), which produced the sequence TPTAELR that start at position 111 of the protein to which it is a hit, and is on the first cell of the particular spreadsheet row.
