Isoelectric Point vs Birdathon

Isoelectric Point (IEP) helps to estimate the charge of macromolecule (proteins, peptides, amino acids, DNA, etc.), consisting of basic and acidic residues as a function of pH value of solution. The application graphically represents the charge fluctuation over the whole range of pH values and finds out the isoelectric point value. The application can extract the protein sequence (chain by chain) from FASTA files. Layout of "IEP".  The sequence of polymer molecule can be typed into the “Sequence” field in the single letter format (YHRK…). Alternatively, it can be uploaded from the PDB-styled FASTA file (for polypeptides) located in "Documents/IEP" folder. Pressing “Load” bar button launches file browser that lets the user to choose the FASTA file. Simple press on 'Chain' button launches chain picker dialog if multiple chains are defined in FASTA file. If peptide is analysed, then tapping “Analyse” button, calculates the molar weight, counts and fills in the number of recognized acidic and basic residues into the appropriate cells in the amino acid info table. Cells for acidic residues are coloured red and for basic are blue. Each row provides three cells: 1. compound (amino acid) name or acronym. 2. pKa value (user defined), default values are provided. 3. Number of the particular residues in the macromolecule. The “-C” and “-N” cells represent standard C- and N-terminus respectively. If peptide has been terminally modified, then these fields data must be changed accordingly. The “Calculate” button initiates the analysis of the table data and outputs the IEP value. Important! Table data can be fully customized after or without any sequence analysis! IEP calculation uses table values, whatever their origin is . Long press on 'Reset' button removes amino acid data from table if the analysed molecule is not based on amino acid sequence or alternatively brings it back if peptide is analysed. Short Tap on reset button simply resets data in table. Application provides data for most common acidic and basic amino acid residues, but every cell can be updated! Sequence analysis reverts the table back to its original state. Important points: Special attention should be paid for number of -C and -N termini and their pKa values, as they depend on functional derivaterization and number of chains being analysed. If user updates any of the data cells, the program will not start to plot until user press calculate button and only if the update is accepted. The cells are colored according to the data input allowed (unchangeable): red for acidic and blue for basic function. However both acidic and basic residue chemical groups are usually provided with pKa values. In case that pKb value is provided, it can be easily converted to pKa using: pKa=pKw-pKb or pKa=14-pKb (at 25°C). User should check what the primary chemical property of the residue is: the proton donor, gaining negative charge (acidic) or proton acceptor, gaining positive charge (basic). Unrecognized amino acid residue letters are skipped, but can be added manually to the available cells. The empty cell sets are available for custom input. The pKa values can be changed in table to fit the desired model. The application assumes no influence between residues. The application assigns dot as a decimal separator.

Birdathon is an observation-centric tool for creating birding checklists. It helps you organize your checklists and share them with others. Use Birdathon in the field to quickly record whether and where a bird is seen or heard and the number observed. The time and location of each observation is automatically recorded. You can adjust the location, time entries and the count of birds observed at any time to ensure your records are accurate. You can add breeding codes to your observations. Checklist maps display the locations of your observations. You can overlay county boundaries for every US state. You can add a range circle such as a 5MR (5-mile Radius) to your maps. You can import and overlay custom kml/kmz files onto your maps. An Overview feature lets you see your combined observations for any time period, and displays a map showing any boundaries you have selected, so you can utilize the map feature even when you are not actively checklisting. You can export Overview data into a csv text file or create a new checklist template from the Overview. Your checklists can be viewed in taxonomic order, alphabetically, by rarity or as a timeline of species. You can enrich your checklist with field notes and add observations such as mammals, butterflies, wildflowers, etc., to make it a more complete record of your experience. You can organize your checklists into categories such as Day List, Year List, County List, Life List, etc., and assign color themes to your lists. Bird species may be added and deleted from your lists at any time. You can create new checklist templates from your previous lists or import templates created by others. You can change which template is being used. You can import text files into Birdathon, making them into templates or new checklists. Different export options for your checklists allow you to import into eBird or another copy of Birdathon. The bird species source data and other resources used in this app come from the following sources: AviList, a unified global checklist of birds, is the core data set used for Birdathon. https://www.avilist.org. Some data has been integrated from the following sources: The eBird/Clements checklist of birds of the world (https://www.birds.cornell.edu/clementschecklist/download/), the American Ornithological Society's (AOS) Checklist of North and Middle American Birds (https://checklist.americanornithology.org), and the American Birding Association's (ABA) checklist of North American Birds (https://www.aba.org/listing-taxonomy/) Alpha codes come from The Institute for Bird Populations’ Standardized 4- and 6-letter Bird Species Codes. https://www.birdpop.org/pages/birdSpeciesCodes.php. County boundary data is from the United States Geological Survey (USGS) TIGER/Line 2019 Shapefiles found on the United States Census Bureau's website at https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.2019.html. Boundaries should be used as general guidelines and not be considered precise. Note especially where county boundaries follow creeks, rivers, ridge lines and other natural features, and so are of much finer resolution than can be shown on Birdathon’s maps. California breeding bird atlas blocks come from the California Bird Atlas, https://www.californiabirdatlas.org. California Bird Atlas logo and breeding code descriptions used with permission.