PMC

Screenshot of PCR real time information file in .csv format. The alphanumeric string "STDi" (with i = 1, 2,...I) identifies each of the I standards and the character string "sample" identifies the unknown sample under investigation. In "target_num" variable, the number i (with i = 1, 2...I) corresponds to each i-th standard and the alphanumeric string "NA" corresponds to the unknown sample. The "ct" variable represents the ct values measured for standards and unknown sample, while the "conc" variable reports the known concentration (copy number) of the standards. Note that, the alphanumeric string NA is inserted in correspondence of the unknown sample. In "rep" variable the number j (with j = 1, 2,...J) identifies each replication for both standards and sample.

Output of the CoCoMac plugin: a the axonal projections of region PHT00-25 are displayed as markers with a color intensity that represents connection strength. Note that this strength measure is not an official CoCoMac variable, it is provided to display capabilities of the SBA; b tabular output, in which each connection is represented by a character string. Each character is a separate ‘piece of evidence’, whereby X,0,1,2,3 mean unknown strength, absent, weak, medium and strong tracer labelling, respectively; c Interactive tabular display at the CoCoMac.g-node.org website allows traceback to the original publication

Identifying breakpoints using split-read information. In the reference genome (bottom), there is one copy of each of Region 1 and Region 2. However, in the sequenced genome (top), Region 1 is deleted and Region 2 is duplicated. For deletions, CIGAR strings of left breakpoints have a string of bases containing the S character on the right while those of right breakpoints have a string of S characters on the left (Supplementary Table ). The S characters are represented by gray.

ProtaBank database schema showing the table for experimental data represented by a number (data_expfdatum, blue header) and all tables with foreign key relationships to it. Each table shows the field name (left) and the variable type for the field (right). Each datum in the data_expfdatum table has a foreign key relationship (orange arrow) to a study table (study_study) that organizes the context in which the experiments were performed, an assay table (assay_expassay) that describes the procedure used to obtain the measurement, a sequence table (sequence_complex) that holds the protein sequence of the mutant, and a units table (data_unit) that describes the units of the result. For data that is part of a mutant library, a foreign key links it to the library table (data_libexpfdatum). Analogous tables exist for data obtained from computations/simulations, derived data, and qualitative or range data. uuid, universally unique ID; avail_date, date study is available for public; seqstr, sequence string; temp, temperature; prot_conc, protein concentration; timestamptz, time stamp with time zone; varchar, variable character; bool, boolean; int, integer; float, floating point number; fk, foreign key.